#include <SimpleInteractionGraph.hh>

Public Member Functions
	SimpleNode (graph::Graph *owner, Size resnum)

virtual	~SimpleNode ()

virtual void	copy_from (graph::Node const *)
	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...

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

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

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

Real	one_body_energy () const

Real	proposed_one_body_energy () const

Real	current_one_body_energy () const

bool	moved () const
	Is this node considering a state substitution? More...

void	commit_change ()
	Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges. More...

void	commit_change_no_res_pointer_update ()
	Copy the alternate energies to the current energies for this node and its incident edges. More...

void	reject_change ()
	Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation. More...

void	set_current (conformation::ResidueCOP res)
	Set the current residue COP, and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "current" energies. More...

void	set_alternate (conformation::ResidueCOP res)
	Set the alternate residue COP and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "proposed" energies. More...

void	set_current_no_E_update (conformation::ResidueCOP res)
	Passive mode behavior: set the current residue pointer without updating the current one body or two body energies. More...

void	set_alternate_no_E_update (conformation::ResidueCOP res)
	Passive mode behavior: set the current residue pointer without updating the alternate one body or proposed two body energies. More...

void	update_energies_after_passive_change ()

conformation::ResidueCOP	get_current () const
	return the pointer to the current state (might be 0) More...

conformation::ResidueCOP	get_alternate () const
	return the pointer to the alternate state (might be 0) More...

Vector const &	bb_centroid () const

Real	bb_radius () const

Vector const &	curr_sc_centroid () const

Real	curr_sc_radius () const

Vector const &	alt_sc_centroid () const

Real	alt_sc_radius () const

Public Member Functions inherited from core::graph::Node
virtual	~Node ()
	virtual destructor More...

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

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...

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

Private Member Functions
void	update_current_one_body_energy ()

void	update_alternate_one_body_energy ()

void	initialize ()

Additional Inherited Members
Public Types inherited from core::graph::Node
typedef EdgeListIterator	EdgeListIter

typedef EdgeListConstIterator	EdgeListConstIter

Protected Member Functions inherited from core::graph::Node
Graph *	get_owner () const
	derived class access to the owner More...

Constructor & Destructor Documentation

core::pack::interaction_graph::SimpleNode::SimpleNode	(	graph::Graph *	owner,
		Size	resnum
	)

References initialize().

core::pack::interaction_graph::SimpleNode::~SimpleNode ( )

virtual

Member Function Documentation

Vector const & core::pack::interaction_graph::SimpleNode::alt_sc_centroid ( ) const

References alt_sc_centroid_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

Real core::pack::interaction_graph::SimpleNode::alt_sc_radius ( ) const

References alt_sc_radius_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

Vector const & core::pack::interaction_graph::SimpleNode::bb_centroid ( ) const

References bb_centroid_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

Real core::pack::interaction_graph::SimpleNode::bb_radius ( ) const

References bb_radius_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

void core::pack::interaction_graph::SimpleNode::commit_change ( )

Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges.

References alternate_residue_, commit_change_no_res_pointer_update(), and current_residue_.

void core::pack::interaction_graph::SimpleNode::commit_change_no_res_pointer_update ( )

Copy the alternate energies to the current energies for this node and its incident edges.

References alternate_one_body_energy_, core::pack::interaction_graph::SimpleEdge::commit_change(), current_one_body_energy_, core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), and moved_.

Referenced by commit_change().

virtual void core::pack::interaction_graph::SimpleNode::copy_from ( graph::Node const * source )

inlinevirtual

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 from core::graph::Node.

virtual platform::Size core::pack::interaction_graph::SimpleNode::count_dynamic_memory ( ) const

inlinevirtual

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 from core::graph::Node.

virtual platform::Size core::pack::interaction_graph::SimpleNode::count_static_memory ( ) const

inlinevirtual

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 from core::graph::Node.

Vector const & core::pack::interaction_graph::SimpleNode::curr_sc_centroid ( ) const

References curr_sc_centroid_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

Real core::pack::interaction_graph::SimpleNode::curr_sc_radius ( ) const

References curr_sc_radius_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

Real core::pack::interaction_graph::SimpleNode::current_one_body_energy ( ) const

References current_one_body_energy_.

Referenced by core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution().

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::get_alternate ( ) const

return the pointer to the alternate state (might be 0)

References alternate_residue_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::get_current ( ) const

return the pointer to the current state (might be 0)

References current_residue_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().

void core::pack::interaction_graph::SimpleNode::initialize ( )

private

Referenced by SimpleNode().

bool core::pack::interaction_graph::SimpleNode::moved ( ) const

Is this node considering a state substitution?

References moved_.

Referenced by core::pack::interaction_graph::SimpleEdge::update_proposed_energy().

Real core::pack::interaction_graph::SimpleNode::one_body_energy ( ) const

References alternate_one_body_energy_, current_one_body_energy_, and moved_.

Referenced by core::pack::interaction_graph::SimpleInteractionGraph::total_energy().

virtual void core::pack::interaction_graph::SimpleNode::print ( ) const

inlinevirtual

send summaray data about this node to the screen

virtual function to print node to standard out

Reimplemented from core::graph::Node.

Real core::pack::interaction_graph::SimpleNode::proposed_one_body_energy ( ) const

References alternate_one_body_energy_.

Referenced by core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), and core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution().

void core::pack::interaction_graph::SimpleNode::reject_change ( )

Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation.

References moved_.

void core::pack::interaction_graph::SimpleNode::set_alternate ( conformation::ResidueCOP res )

Set the alternate residue COP and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "proposed" energies.

References alt_sc_centroid_, alt_sc_radius_, alternate_residue_, core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), moved_, core::pack::interaction_graph::TR, update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleEdge::update_proposed_energy().

Referenced by core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution().

void core::pack::interaction_graph::SimpleNode::set_alternate_no_E_update ( conformation::ResidueCOP res )

Passive mode behavior: set the current residue pointer without updating the alternate one body or proposed two body energies.

References alternate_residue_, and moved_.

void core::pack::interaction_graph::SimpleNode::set_current ( conformation::ResidueCOP res )

Set the current residue COP, and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "current" energies.

References bb_centroid_, bb_radius_, core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), curr_sc_centroid_, curr_sc_radius_, current_residue_, core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), moved_, core::pack::interaction_graph::SimpleEdge::update_current_energy(), and update_current_one_body_energy().

Referenced by core::pack::interaction_graph::SimpleInteractionGraph::initialize(), and core::pack::interaction_graph::SimpleInteractionGraph::set_pose_no_initialize().

void core::pack::interaction_graph::SimpleNode::set_current_no_E_update ( conformation::ResidueCOP res )

Passive mode behavior: set the current residue pointer without updating the current one body or two body energies.

References current_residue_.

void core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy ( )

private

References alternate_one_body_energy_, alternate_residue_, core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_1b(), core::scoring::ScoreFunction::eval_cd_intrares_energy(), core::scoring::ScoreFunction::eval_ci_1b(), core::scoring::ScoreFunction::eval_ci_intrares_energy(), core::graph::Node::get_owner(), core::pack::interaction_graph::SimpleInteractionGraph::pose(), core::pack::interaction_graph::SimpleInteractionGraph::scorefunction(), and core::scoring::ScoreFunction::weights().

Referenced by set_alternate(), and update_energies_after_passive_change().

void core::pack::interaction_graph::SimpleNode::update_current_one_body_energy ( )

private

References current_one_body_energy_, current_residue_, core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_1b(), core::scoring::ScoreFunction::eval_cd_intrares_energy(), core::scoring::ScoreFunction::eval_ci_1b(), core::scoring::ScoreFunction::eval_ci_intrares_energy(), core::graph::Node::get_owner(), core::pack::interaction_graph::SimpleInteractionGraph::pose(), runtime_assert, core::pack::interaction_graph::SimpleInteractionGraph::scorefunction(), and core::scoring::ScoreFunction::weights().

Referenced by set_current().

void core::pack::interaction_graph::SimpleNode::update_energies_after_passive_change ( )

References core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleEdge::update_proposed_energy().

Member Data Documentation

Vector core::pack::interaction_graph::SimpleNode::alt_sc_centroid_

private

Referenced by alt_sc_centroid(), and set_alternate().

Real core::pack::interaction_graph::SimpleNode::alt_sc_radius_

private

Referenced by alt_sc_radius(), and set_alternate().

Real core::pack::interaction_graph::SimpleNode::alternate_one_body_energy_

private

Referenced by commit_change_no_res_pointer_update(), one_body_energy(), proposed_one_body_energy(), and update_alternate_one_body_energy().

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::alternate_residue_

private

Referenced by commit_change(), get_alternate(), set_alternate(), set_alternate_no_E_update(), and update_alternate_one_body_energy().

Vector core::pack::interaction_graph::SimpleNode::bb_centroid_

private

Referenced by bb_centroid(), and set_current().

Real core::pack::interaction_graph::SimpleNode::bb_radius_

private

Referenced by bb_radius(), and set_current().

Vector core::pack::interaction_graph::SimpleNode::curr_sc_centroid_

private

Referenced by curr_sc_centroid(), and set_current().

Real core::pack::interaction_graph::SimpleNode::curr_sc_radius_

private

Referenced by curr_sc_radius(), and set_current().

Real core::pack::interaction_graph::SimpleNode::current_one_body_energy_

private

Referenced by commit_change_no_res_pointer_update(), current_one_body_energy(), one_body_energy(), and update_current_one_body_energy().

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::current_residue_

private

Referenced by commit_change(), get_current(), set_current(), set_current_no_E_update(), and update_current_one_body_energy().

bool core::pack::interaction_graph::SimpleNode::moved_

private

Referenced by commit_change_no_res_pointer_update(), moved(), one_body_energy(), reject_change(), set_alternate(), set_alternate_no_E_update(), and set_current().

Size core::pack::interaction_graph::SimpleNode::resnum_

private

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

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

Private Attributes
bool	moved_

Size	resnum_

Real	current_one_body_energy_

Real	alternate_one_body_energy_

conformation::ResidueCOP	current_residue_

conformation::ResidueCOP	alternate_residue_

Vector	bb_centroid_

Real	bb_radius_

Vector	curr_sc_centroid_

Real	curr_sc_radius_

Vector	alt_sc_centroid_

Real	alt_sc_radius_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation