#include <Graph.hh>

Public Types
typedef EdgeListIterator	EdgeListIter

typedef EdgeListConstIterator	EdgeListConstIter

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

	Node (Graph *, platform::Size node_id)
	Main constructor, no default constructor nor copy constructor. More...

virtual void	copy_from (Node const *source)
	invoked during graph assignment operators to copy any node data from one graph to another graph. The source node must be the same type as this node. More...

void	add_edge (Edge *edge_ptr, EdgeListIter &)
	adds edge pointer to edge list; returns an iterator to the new list element More...

void	drop_edge (EdgeListIter edge_iterator)
	removes an edge iterator from the node's edge list. Only called by Edge class. More...

void	drop_all_edges ()
	deletes all edges incident upon this node More...

void	set_num_neighbors_counting_self_static (platform::Size neighbor)

Edge const *	find_edge (platform::Size other_node_index) const
	a "slow" (linear) search for an edge. More...

Edge *	find_edge (platform::Size other_node_index)
	non-const edge finding method; changes no data, but returns a non-const pointer More...

virtual void	print () const
	send summaray data about this node to the screen More...

EdgeListIter	edge_list_begin ()
	returns a non-const iterator to the beginning of its edge list More...

EdgeListConstIter	const_edge_list_begin () const
	returns a const iterator to the beginning of its edge list More...

EdgeListIter	edge_list_end ()
	returns a non-const iterator to the end of its edge list More...

EdgeListConstIter	const_edge_list_end () const
	returns a const iterator to the end of its edge list More...

EdgeListIter	lower_edge_list_begin ()
	returns a non-const iterator to the beginning of its lower-edge list More...

EdgeListConstIter	const_lower_edge_list_begin () const
	returns a const iterator to the beginning of its lower-edge list More...

EdgeListIter	lower_edge_list_end ()
	returns a non-const iterator to the end of its lower-edge list More...

EdgeListConstIter	const_lower_edge_list_end () const
	returns a const iterator to the end of its lower-edge list More...

EdgeListIter	upper_edge_list_begin ()
	returns a non-const iterator to the beginning of its upper-edge list More...

EdgeListConstIter	const_upper_edge_list_begin () const
	returns a const iterator to the beginning of its upper-edge list More...

EdgeListIter	upper_edge_list_end ()
	returns a non-const iterator to the end of its upper-edge list More...

EdgeListConstIter	const_upper_edge_list_end () const
	returns a const iterator to the end of its upper-edge list More...

platform::Size	get_node_index () const
	the index for this node More...

platform::Size	num_edges () const
	the number of edges incident on this node, which may include a loop edge More...

platform::Size	num_neighbors_counting_self () const
	the number of neighbors counting "self" as a neighbor. More...

platform::Size	num_neighbors_counting_self_static () const
	the number of neighbors counting "self" as neighbor. Defaults to num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures. More...

platform::Size	get_num_edges_to_smaller_indexed_nodes () const
	the number of lower neighbors More...

platform::Size	get_num_edges_to_larger_indexed_nodes () const
	the number of upper neighbors – which "self" neighborness is counted if a loop edge is present More...

virtual platform::Size	count_static_memory () const
	memory accounting scheme More...

virtual platform::Size	count_dynamic_memory () const
	memory accounting scheme More...

bool	loop_incident () const
	NOTE TO SELF: remove loop support. More...

Protected Member Functions
Graph *	get_owner () const
	derived class access to the owner More...

Private Member Functions
	Node ()

	Node (Node const &)

Node &	operator= (Node &)

Private Attributes
platform::Size	node_index_

platform::Size	num_incident_edges_

platform::Size	num_neighbors_counting_self_static_

bool	loop_incident_

platform::Size	num_edges_to_smaller_indexed_nodes_
	NOTE TO SELF: remove loop support. More...

platform::Size	num_edges_to_larger_indexed_nodes_

EdgeList	incident_edge_list_

EdgeListIter	first_upper_edge_

Graph *	owner_

Member Typedef Documentation

typedef EdgeListConstIterator core::graph::Node::EdgeListConstIter

typedef EdgeListIterator core::graph::Node::EdgeListIter

Constructor & Destructor Documentation

core::graph::Node::~Node ( )

virtual

virtual destructor

core::graph::Node::Node	(	Graph *	owner,
		platform::Size	node_id
	)

Main constructor, no default constructor nor copy constructor.

core::graph::Node::Node ( )

private

Referenced by count_static_memory().

core::graph::Node::Node ( Node const & )

private

Member Function Documentation

void core::graph::Node::add_edge	(	Edge *	edge_ptr,
		EdgeListIter &	eiter
	)

adds edge pointer to edge list; returns an iterator to the new list element

If the other node this node is attached to by edge_ptr has a higher index then the edge is added to the end of its edge list; if the node has a smaller index, the edge pointer is added to the front of the edge list. The presence of a new edge means the edge vector is not up to date.

Parameters

edge_ptr - [in] - the new edge

References core::graph::EdgeList::begin(), core::graph::EdgeList::end(), first_upper_edge_, core::graph::Edge::get_other_ind(), incident_edge_list_, core::graph::EdgeList::insert(), core::graph::Edge::is_loop(), loop_incident_, node_index_, num_edges_to_larger_indexed_nodes_, num_edges_to_smaller_indexed_nodes_, num_incident_edges_, num_neighbors_counting_self(), and num_neighbors_counting_self_static_.

EdgeListConstIter core::graph::Node::const_edge_list_begin ( ) const

inline

returns a const iterator to the beginning of its edge list

References core::graph::EdgeList::const_begin(), and incident_edge_list_.

Referenced by core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::graph::find_connected_components(), core::scoring::TenANeighborNode::neighbor_mass(), core::pack::scmin::CartSCMinMultifunc::operator()(), core::pack::scmin::SCMinMultifunc::operator()(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::pack::RTMin::rtmin(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), and core::scoring::TenANeighborNode::update_neighbor_mass_sum().

EdgeListConstIter core::graph::Node::const_edge_list_end ( ) const

inline

returns a const iterator to the end of its edge list

References core::graph::EdgeList::const_end(), and incident_edge_list_.

EdgeListConstIter core::graph::Node::const_lower_edge_list_begin ( ) const

inline

returns a const iterator to the beginning of its lower-edge list

References core::graph::EdgeList::const_begin(), and incident_edge_list_.

EdgeListConstIter core::graph::Node::const_lower_edge_list_end ( ) const

inline

returns a const iterator to the end of its lower-edge list

References first_upper_edge_.

EdgeListConstIter core::graph::Node::const_upper_edge_list_begin ( ) const

inline

returns a const iterator to the beginning of its upper-edge list

References first_upper_edge_.

EdgeListConstIter core::graph::Node::const_upper_edge_list_end ( ) const

inline

returns a const iterator to the end of its upper-edge list

References core::graph::EdgeList::const_end(), and incident_edge_list_.

Referenced by core::scoring::methods::LK_hack::calculate_derivatives_for_atoms_and_pseudo_base_atoms(), core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::ScoreFunction::get_sub_score(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), core::scoring::FACTSPotential::setup_for_derivatives(), and core::scoring::SecondaryStructurePotential::sspair().

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

virtual

invoked during graph assignment operators to copy any node data from one graph to another graph. The source node must be the same type as this node.

copy-from for use in Graph::operator= and copy ctors; derived classes must define their own version of this function

Reimplemented in core::scoring::MinimizationNode, core::scoring::EnergyNode, core::pack::interaction_graph::SimpleNode, core::scoring::TenANeighborNode, core::scoring::TwelveANeighborNode, and core::scoring::constraints::ConstraintNode.

Referenced by core::scoring::constraints::ConstraintNode::copy_from().

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

virtual

memory accounting scheme

recursively descend through heirarchy accounting for heap memory usage. Each derived class in the heirarchy should recursively add the amount of dynamic memory its parent allocates by calling parent::count_dynamic_memory

Reimplemented in core::scoring::MinimizationNode, core::scoring::EnergyNode, core::pack::interaction_graph::SimpleNode, core::scoring::TenANeighborNode, core::scoring::TwelveANeighborNode, and core::scoring::constraints::ConstraintNode.

References num_incident_edges_.

Referenced by core::scoring::constraints::ConstraintNode::count_dynamic_memory(), core::scoring::TwelveANeighborNode::count_dynamic_memory(), core::scoring::TenANeighborNode::count_dynamic_memory(), core::scoring::EnergyNode::count_dynamic_memory(), and core::scoring::MinimizationNode::count_dynamic_memory().

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

virtual

memory accounting scheme

called on most-derived class. The most-derived class should NOT recursively call this method on its parent class. The sizeof function will handle the whole Node (or DerivedNode).

Reimplemented in core::scoring::MinimizationNode, core::scoring::EnergyNode, core::pack::interaction_graph::SimpleNode, core::scoring::TenANeighborNode, core::scoring::TwelveANeighborNode, and core::scoring::constraints::ConstraintNode.

References Node().

void core::graph::Node::drop_all_edges ( )

deletes all edges incident upon this node

As edges delete themselves, they invalidate any iterators that point to their (former) positions in the node and graph edge lists. Therefore, before calling delete on an edge object, one must grab the next iterator in a list. Below, nextiter copies iter and is incremented before iter's edge is deleted. Note also that "++iter" does not appear in the for loop.

References core::graph::EdgeList::begin(), core::graph::Graph::delete_edge(), core::graph::EdgeList::end(), incident_edge_list_, and owner_.

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

void core::graph::Node::drop_edge ( EdgeListIter eiter )

removes an edge iterator from the node's edge list. Only called by Edge class.

edges efficiently delete themselves from the edge lists of the nodes they are incident upon by keeping a pair of iterators. Edges request nodes delete them by handing the iterator back to the node.

Parameters

edge	- [in] - the iterator for this node's edge list that points at the edge which is trying to delete itself

References core::graph::EdgeList::erase(), first_upper_edge_, core::graph::Edge::get_other_ind(), incident_edge_list_, loop_incident_, node_index_, num_edges_to_larger_indexed_nodes_, num_edges_to_smaller_indexed_nodes_, num_incident_edges_, num_neighbors_counting_self(), and num_neighbors_counting_self_static_.

Referenced by core::graph::Edge::~Edge().

EdgeListIter core::graph::Node::edge_list_begin ( )

inline

returns a non-const iterator to the beginning of its edge list

References core::graph::EdgeList::begin(), and incident_edge_list_.

Referenced by core::pack::interaction_graph::SimpleNode::commit_change_no_res_pointer_update(), core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::operator()(), core::pack::scmin::SCMinMultifunc::operator()(), core::pack::reinitialize_mingraph_neighborhood_for_residue(), core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), and core::pack::interaction_graph::SimpleNode::update_energies_after_passive_change().

EdgeListIter core::graph::Node::edge_list_end ( )

inline

returns a non-const iterator to the end of its edge list

References core::graph::EdgeList::end(), and incident_edge_list_.

Referenced by core::pack::interaction_graph::SimpleNode::commit_change_no_res_pointer_update(), core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::operator()(), core::pack::scmin::SCMinMultifunc::operator()(), core::pack::reinitialize_mingraph_neighborhood_for_residue(), core::pack::RTMin::rtmin(), core::pack::interaction_graph::SimpleNode::set_alternate(), core::pack::interaction_graph::SimpleNode::set_current(), and core::pack::interaction_graph::SimpleNode::update_energies_after_passive_change().

Edge const * core::graph::Node::find_edge ( platform::Size other_node ) const

a "slow" (linear) search for an edge.

Constant time if each vertex has a constant number of edges. Edges are identified by the index of the node to which the edge connects this node. Returns NULL when there is no such connecting edge.

Parameters

other_node - [in] - the index of the node that the desired edge connects this node to

Edge * core::graph::Node::find_edge ( platform::Size other_node_index )

non-const edge finding method; changes no data, but returns a non-const pointer

References core::graph::EdgeList::begin(), core::sequence::end, core::graph::EdgeList::end(), first_upper_edge_, get_node_index(), incident_edge_list_, node_index_, and start.

platform::Size core::graph::Node::get_node_index ( ) const

inline

the index for this node

References node_index_.

Referenced by find_edge(), core::scoring::TenANeighborNode::neighbor_mass(), print(), and core::scoring::TenANeighborNode::update_neighbor_mass_sum().

platform::Size core::graph::Node::get_num_edges_to_larger_indexed_nodes ( ) const

inline

the number of upper neighbors – which "self" neighborness is counted if a loop edge is present

References num_edges_to_larger_indexed_nodes_.

platform::Size core::graph::Node::get_num_edges_to_smaller_indexed_nodes ( ) const

inline

the number of lower neighbors

References num_edges_to_smaller_indexed_nodes_.

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

inlineprotected

derived class access to the owner

References owner_.

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

bool core::graph::Node::loop_incident ( ) const

inline

NOTE TO SELF: remove loop support.

References loop_incident_.

EdgeListIter core::graph::Node::lower_edge_list_begin ( )

inline

returns a non-const iterator to the beginning of its lower-edge list

References core::graph::EdgeList::begin(), and incident_edge_list_.

EdgeListIter core::graph::Node::lower_edge_list_end ( )

inline

returns a non-const iterator to the end of its lower-edge list

References first_upper_edge_.

platform::Size core::graph::Node::num_edges ( ) const

inline

the number of edges incident on this node, which may include a loop edge

References num_incident_edges_.

platform::Size core::graph::Node::num_neighbors_counting_self ( ) const

inline

the number of neighbors counting "self" as a neighbor.

References loop_incident_, and num_incident_edges_.

Referenced by add_edge(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), drop_edge(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::pack::interaction_graph::SurfaceNode< V, E, G >::initialize_num_neighbors_counting_self(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::initialize_num_neighbors_counting_self(), and core::io::sequence_comparation::DesignContrast::setNeighbors().

platform::Size core::graph::Node::num_neighbors_counting_self_static ( ) const

inline

the number of neighbors counting "self" as neighbor. Defaults to num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures.

References num_neighbors_counting_self_static_.

Referenced by core::scoring::hbonds::fill_hbond_set().

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

private

void core::graph::Node::print ( ) const

virtual

send summaray data about this node to the screen

virtual function to print node to standard out

Reimplemented in core::scoring::MinimizationNode, core::scoring::EnergyNode, and core::pack::interaction_graph::SimpleNode.

References core::graph::EdgeList::const_begin(), core::graph::EdgeList::const_end(), get_node_index(), and incident_edge_list_.

Referenced by core::scoring::EnergyNode::print(), and core::scoring::MinimizationNode::print().

void core::graph::Node::set_num_neighbors_counting_self_static ( platform::Size neighbor )