core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > Class Template Reference

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 >:

Collaboration 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...

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

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_

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.

BackgroundToFirstClassEdge

Detailed:

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.

Definition at line 37 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 269 of file AdditionalBackgroundNodesInteractionGraph.hh.

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.

BackgroundToFirstClassEdge::~BackgroundToFirstClassEdge

Definition at line 801 of file AdditionalBackgroundNodesInteractionGraph.hh.

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 =.

BackgroundToFirstClassEdge::BackgroundToFirstClassEdge

Detailed:

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

Definition at line 780 of file AdditionalBackgroundNodesInteractionGraph.hh.

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 >

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.

BackgroundToFirstClassEdge::count_dynamic_memory

Remarks

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

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

Definition at line 963 of file AdditionalBackgroundNodesInteractionGraph.hh.

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 >, 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

Definition at line 303 of file AdditionalBackgroundNodesInteractionGraph.hh.

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(), 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

Definition at line 279 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 300 of file AdditionalBackgroundNodesInteractionGraph.hh.

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(), 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

Definition at line 276 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

BackgroundToFirstClassEdge::get_other_ind

Detailed:

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.

Definition at line 823 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

BackgroundToFirstClassEdge::get_other_ind

Detailed:

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.

Definition at line 843 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

BackgroundToFirstClassEdge::get_other_node

Detailed:

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()

Definition at line 875 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

BackgroundToFirstClassEdge::get_other_node

Detailed:

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()

Definition at line 859 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

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

inlineprotected

Definition at line 306 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

BackgroundToFirstClassEdge::same_edge

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.

Definition at line 949 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

BackgroundToFirstClassEdge::set_pos_in_node_edgevector

Detailed:

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

Definition at line 909 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

BackgroundToFirstClassEdge::set_pos_in_node_edgevector

Detailed:

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

Definition at line 928 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::set_pos_in_owners_list

(

BackgroundEdgeListIter

iter)

stores the iterator to this edge in the owning graph's list of background-to-first-class edges.

BackgroundToFirstClassEdge::set_pos_in_owners_list

Detailed:

required for constant time edge deletion

Definition at line 890 of file AdditionalBackgroundNodesInteractionGraph.hh.

Referenced by core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::add_background_edge().

Member Data Documentation

template<typename V, typename E, typename G>

BackgroundNode< V, E, G >* core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::background_node_

private

Definition at line 314 of file AdditionalBackgroundNodesInteractionGraph.hh.

Referenced by core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_background_node().

template<typename V, typename E, typename G>

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

private

Definition at line 311 of file AdditionalBackgroundNodesInteractionGraph.hh.

Referenced by core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_background_node_index().

template<typename V, typename E, typename G>

FirstClassNode< V, E, G >* core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::first_class_node_

private

Definition at line 313 of file AdditionalBackgroundNodesInteractionGraph.hh.

Referenced by core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_first_class_node().

template<typename V, typename E, typename G>

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

private

Definition at line 310 of file AdditionalBackgroundNodesInteractionGraph.hh.

Referenced by core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_first_class_node_index().

template<typename V, typename E, typename G>

AdditionalBackgroundNodesInteractionGraph< V, E, G >* core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::owner_

private

Definition at line 322 of file AdditionalBackgroundNodesInteractionGraph.hh.

Referenced by core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::get_owner().

template<typename V, typename E, typename G>

int core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::pos_in_bg_edge_vector_

private

Definition at line 317 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

BackgroundEdgeListIter core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::pos_in_bg_nodes_edge_list_

private

Definition at line 319 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::pos_in_fc_edge_vector_

private

Definition at line 316 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

BackgroundEdgeListIter core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::pos_in_fc_nodes_edge_list_

private

Definition at line 318 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

BackgroundEdgeListIter core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >::pos_in_owners_edge_list_

private

Definition at line 320 of file AdditionalBackgroundNodesInteractionGraph.hh.

---

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

• src/core/pack/interaction_graph/AdditionalBackgroundNodesInteractionGraph.hh