An edge between a background node and a first class node. More...

#include <AdditionalBackgroundNodesInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >:

Public Types
typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >::iterator	BackgroundEdgeListIter

Public Member Functions
virtual	~BackgroundToFirstClassEdge ()
	virtual destructor. The edge removes itself from the graph by informing the two vertices its incident upon to drop it from their edge lists. Constant time edge removal. More...

	BackgroundToFirstClassEdge (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int fc_node_index, int bg_node_index)
	BackgroundToFirstClassEdge constructor - no default or copy constructors; no operator =. More...

int	get_first_class_node_index () const

int	get_background_node_index () const

int	get_other_ind (FirstClassNode< V, E, G > *) const
	returns the index of the second class node More...

int	get_other_ind (BackgroundNode< V, E, G > *) const
	returns the index of the first class node More...

FirstClassNode< V, E, G > *	get_other_node (BackgroundNode< V, E, G > *) const
	returns a pointer to the first class node More...

BackgroundNode< V, E, G > *	get_other_node (FirstClassNode< V, E, G > *) const
	returns a pointer to the second class node More...

void	set_pos_in_owners_list (BackgroundEdgeListIter)
	stores the iterator to this edge in the owning graph's list of background-to-first-class edges. More...

void	set_pos_in_node_edgevector (FirstClassNode< V, E, G > *caller, int pos)
	stores the index of this edge in its first class node's edge vector More...

void	set_pos_in_node_edgevector (BackgroundNode< V, E, G > *caller, int pos)
	stores the index of this edge in its second class node's edge vector More...

bool	same_edge (int fc_node_index, int bg_node_index) const
	returns true if this node is incident upon the two input vertex indices More...

virtual void	prepare_for_simulated_annealing ()=0

virtual unsigned int	count_static_memory () const =0

virtual unsigned int	count_dynamic_memory () const
	Returns an int representing the amount of memory in bytes used by this node. More...

bool	bgtfce_marked_for_deletion ()

Protected Member Functions
FirstClassNode< V, E, G > *	get_first_class_node () const

BackgroundNode< V, E, G > *	get_background_node () const

AdditionalBackgroundNodesInteractionGraph < V, E, G > *	get_owner () const

void	bgtfce_mark_edge_for_deletion ()

Private Member Functions
	BackgroundToFirstClassEdge ()

	BackgroundToFirstClassEdge (BackgroundToFirstClassEdge< V, E, G > const &)

BackgroundToFirstClassEdge< V, E, G > &	operator= (BackgroundToFirstClassEdge< V, E, G > const &)

Private Attributes
int	first_class_node_index_

int	background_node_index_

FirstClassNode< V, E, G > *	first_class_node_

BackgroundNode< V, E, G > *	background_node_

int	pos_in_fc_edge_vector_

int	pos_in_bg_edge_vector_

BackgroundEdgeListIter	pos_in_fc_nodes_edge_list_

BackgroundEdgeListIter	pos_in_bg_nodes_edge_list_

BackgroundEdgeListIter	pos_in_owners_edge_list_

AdditionalBackgroundNodesInteractionGraph < V, E, G > *	owner_

bool	marked_for_deletion_ = false

Detailed Description

template<typename V, typename E, typename G>
class core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >

An edge between a background node and a first class node.

Remarks: Only derived classes can get non-const access to the FirstClassNode and BackgroundNode members. Const access is provided as a public method. Non-instantiable due to pure virtual methods. Not sure what the 'pos_in_fc_nodes_edge_list_' and other Iterator returning methods are used for.

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef std::list< BackgroundToFirstClassEdge< V, E, G >* >::iterator core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::BackgroundEdgeListIter

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::~BackgroundToFirstClassEdge ( )

virtual

virtual destructor. The edge removes itself from the graph by informing the two vertices its incident upon to drop it from their edge lists. Constant time edge removal.

template<typename V , typename E , typename G >

core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::BackgroundToFirstClassEdge	(	AdditionalBackgroundNodesInteractionGraph< V, E, G > *	owner,
		int	fc_node_index,
		int	bg_node_index
	)

BackgroundToFirstClassEdge constructor - no default or copy constructors; no operator =.

This class of edge connects first class and second class nodes. This class of edge is very unlikely to hold the same kind of data in a (concrete) derived class. e.g. The SASABackgroundEdge holds pre-computed rotamer sphere overlaps for each rotamer-on-a-SASANode and the single-(fixed)-rotamer-on-a-background residue. The first class edge does not attempt to store precomputed sphere overlaps as they would be prohibitively expensive.

Parameters

owner - [in] - the owning graph fc_node_index - [in] - the index of the first class node bg_node_index - [in] - the index of the second class node

template<typename V, typename E, typename G>

core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::BackgroundToFirstClassEdge ( )

private

template<typename V, typename E, typename G>

core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::BackgroundToFirstClassEdge ( BackgroundToFirstClassEdge< V, E, G > const & )

private

Member Function Documentation

template<typename V, typename E, typename G>

void core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::bgtfce_mark_edge_for_deletion ( )

inlineprotected

References core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::marked_for_deletion_.

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::bgtfce_marked_for_deletion ( )

inline

References core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::marked_for_deletion_.

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::count_dynamic_memory ( ) const

virtual

Returns an int representing the amount of memory in bytes used by this node.

Remarks: return 0 because no memory is dynamically allocated for these edges.

Reimplemented in core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >, core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >, and core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >.

template<typename V, typename E, typename G>

virtual unsigned int core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::count_static_memory ( ) const

pure virtual

Implemented in core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >, core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >, and core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >.

template<typename V, typename E, typename G>

BackgroundNode< V, E, G >* core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_background_node ( ) const

inlineprotected

References core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::background_node_.

Referenced by core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::get_hpatch_bg_node(), core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::get_npd_hbond_bg_node(), and core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::get_surface_bg_node().

template<typename V, typename E, typename G>

int core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_background_node_index ( ) const

inline

References core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::background_node_index_.

template<typename V, typename E, typename G>

FirstClassNode< V, E, G >* core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_first_class_node ( ) const

inlineprotected

References core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::first_class_node_.

Referenced by core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::get_hpatch_node(), core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::get_npd_hbond_node(), and core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::get_surface_node().

template<typename V, typename E, typename G>

int core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_first_class_node_index ( ) const

inline

References core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::first_class_node_index_.

template<typename V , typename E , typename G >

int core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_other_ind ( FirstClassNode< V, E, G > * ) const

returns the index of the second class node

A first class vertex may request a BackgroundToFirstClassEdge for the index of the background node the edge connects it to by invoking edge->get_other_ind( this ); The this pointer simply tells the compiler which of the two overloaded get_other_ind() methods to invoke.

Parameters

(unnamed parameter) - [in] - First Class nodes want information about second class nodes when they refer to "the other node". The compiler resolves which of the two overloaded methods to invoke.

template<typename V , typename E , typename G >

int core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_other_ind ( BackgroundNode< V, E, G > * ) const

returns the index of the first class node

A second class vertex may request a BackgroundToFirstClassEdge for the index of the first class node the edge connects it to by invoking edge->get_other_ind( this ); The this pointer simply tells the compiler which of the two overloaded get_other_ind() methods to invoke.

Parameters

(unnamed parameter) - [in] - second class nodes want information about first class nodes when they refer to "the other node". The compiler resolves which of the two overloaded methods to invoke.

template<typename V , typename E , typename G >

FirstClassNode< V, E, G > * core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_other_node ( BackgroundNode< V, E, G > * ) const

returns a pointer to the first class node

unnamed parameter is usually the this pointer where the method is invoked inside a method of a second class node. the pointer type must be resolved at compile time. Same ideas here as in get_other_ind()

template<typename V , typename E , typename G >

BackgroundNode< V, E, G > * core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_other_node ( FirstClassNode< V, E, G > * ) const

returns a pointer to the second class node

unnamed parameter is usually the this pointer where the method is invoked inside a method of a first class node. the pointer type must be resolved at compile time. Same ideas here as in get_other_ind()

template<typename V, typename E, typename G>

AdditionalBackgroundNodesInteractionGraph< V, E, G >* core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_owner ( ) const

inlineprotected

References core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::owner_.

Referenced by core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::get_npd_hbond_owner().

template<typename V, typename E, typename G>

BackgroundToFirstClassEdge< V, E, G >& core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::operator= ( BackgroundToFirstClassEdge< V, E, G > const & )

private

template<typename V, typename E, typename G>

virtual void core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::prepare_for_simulated_annealing ( )

pure virtual

Implemented in core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >, core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >, and core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >.

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::same_edge	(	int	fc_node_index,
		int	bg_node_index
	)		const

returns true if this node is incident upon the two input vertex indices

Parameters

fc_node_index - [in] - the index of the first class node bg_node_index - [in] - the index of the second class node

Remarks: This graph setup will not support multigraphs: graphs that include multiple edges to the same vertices. In my (apl) original dynamic programming algorithm I didn't want to support multigraphs either; but in the adaptive dynamic programming implementation, multiple copies of "the same" edge ended up saving time – though maybe not memory. So, this framework here will not readily support adaptive dynamic programming; but that's ok.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::set_pos_in_node_edgevector	(	FirstClassNode< V, E, G > *	caller,
		int	pos
	)

stores the index of this edge in its first class node's edge vector

again, first (unnamed) parameter is the 'this' pointer where the method has been invoked inside a method of the first class node.

Parameters

(unnamed parameter) - [in] - pointer identifying the type of the node that invoked this overloaded method. pos - [in] - the position of 'this' edge in the edge vector of the first class node

template<typename V , typename E , typename G >

void core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::set_pos_in_node_edgevector	(	BackgroundNode< V, E, G > *	caller,
		int	pos
	)

stores the index of this edge in its second class node's edge vector

again, first (unnamed) parameter is the this pointer where the method has been invoked inside a method of the second class node.

Parameters

(unnamed parameter) - [in] - pointer identifying the type of the node that invoked this overloaded method. pos - [in] - the position of this node in the edge vector of the second class node

template<typename V , typename E , typename G >

void core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::set_pos_in_owners_list ( BackgroundEdgeListIter iter )