A node which is not changing type or rotamer throughout a simulation. More...

#include <AdditionalBackgroundNodesInteractionGraph.hh>

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

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

typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >	BackgroundEdgeList

typedef std::vector < BackgroundToFirstClassEdge < V, E, G > * >	BackgroundEdgeVector

typedef std::vector < BackgroundToFirstClassEdge < V, E, G > * >::iterator	BackgroundEdgeVectorIter

typedef std::vector < FirstClassNode< V, E, G > * >	FirstClassNodeVector

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

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

BackgroundEdgeListIter	add_edge (BackgroundToFirstClassEdge< V, E, G > *edge_ptr)
	Adds a BackgroundToFirstClassEdge to the edge list for this node. Returns an iterator to the new list element. More...

void	drop_edge (BackgroundEdgeListIter edge)
	removes an edge from the nodes edge list in constant time More...

BackgroundToFirstClassEdge< V, E, G > *	find_edge (int fc_node_index)
	Linear time edge lookup function. More...

virtual void	prepare_for_simulated_annealing ()=0

virtual void	print () const =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
void	update_edge_vector ()
	Syncs the edge vector with the edge list. More...

int	get_node_index () const

int	get_num_incident_edges () const

BackgroundToFirstClassEdge< V, E, G > *	get_incident_edge (int index) const

int	get_index_of_adjacent_first_class_node (int index) const

FirstClassNode< V, E, G > *	get_adjacent_first_class_node (int index) const

bool	get_edge_vector_up_to_date () const

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

Private Member Functions
	BackgroundNode ()

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

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

Private Attributes
int	node_index_

int	num_incident_edges_

BackgroundEdgeList	edge_list_

BackgroundEdgeVector	edge_vector_

std::vector< int >	adjacent_first_class_node_indices_

FirstClassNodeVector	adjacent_nodes_

bool	edge_vector_up_to_date_

AdditionalBackgroundNodesInteractionGraph < V, E, G > *	owner_

Detailed Description

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

A node which is not changing type or rotamer throughout a simulation.

In the case of solvent-accessible surface area (SASA) scoring, a background node would be one whose SASA score can change due to neighboring residues being changed. It itself will not change residue type or rotamer during a simulation, but the scores on this residue can change.

Remarks: Non-instantiable due to pure virtual methods, prepare_for_simulated_annealing(), print(), and count_static_memory().

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef std::list< BackgroundToFirstClassEdge< V, E, G >* > core::pack::interaction_graph::BackgroundNode< V, E, G >::BackgroundEdgeList

template<typename V, typename E, typename G>

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

template<typename V, typename E, typename G>

typedef std::vector< BackgroundToFirstClassEdge< V, E, G >* > core::pack::interaction_graph::BackgroundNode< V, E, G >::BackgroundEdgeVector

template<typename V, typename E, typename G>

typedef std::vector< BackgroundToFirstClassEdge< V, E, G >* >::iterator core::pack::interaction_graph::BackgroundNode< V, E, G >::BackgroundEdgeVectorIter

template<typename V, typename E, typename G>

typedef std::vector< FirstClassNode< V, E, G >* > core::pack::interaction_graph::BackgroundNode< V, E, G >::FirstClassNodeVector

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

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

virtual

BackgroundNode destructor.

template<typename V , typename E , typename G >

core::pack::interaction_graph::BackgroundNode< V, E, G >::BackgroundNode	(	AdditionalBackgroundNodesInteractionGraph< V, E, G > *	owner,
		int	node_index
	)

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

I use "background node" synonymously with "second class node". This kind of node contributes to the energy of the system. It does not have any assignable states – the energy it contributes is a function of the states of the first class vertices that surround it. A simulated annealer is unaware of the presence of this kind of node; the owning interaction graph obscures it from view of the annealer.

Parameters

owner - [in] - the owning graph node_index - [in] - the index of the background node

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

std::list< BackgroundToFirstClassEdge< V, E, G > * >::iterator core::pack::interaction_graph::BackgroundNode< V, E, G >::add_edge ( BackgroundToFirstClassEdge< V, E, G > * edge_ptr )

Adds a BackgroundToFirstClassEdge to the edge list for this node. Returns an iterator to the new list element.

Remarks: Invalidates edge_vector_up_to_date_ flag

Parameters

edge_ptr - [in] - pointer to the edge being added

template<typename V , typename E , typename G >

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

virtual

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

Remarks: ronj lists consume more memory because they maintain pointers to the previous and next nodes ronj current calculation uses 4 * # elements in list * sizeof(pointer), but I think this is wrong ronj isn't it only 3 * # elements in list * sizeof(pointer)?

Parameters

total_memory - [out] - the amount of memory used by this node

Reimplemented in core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >, core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >, and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >.

template<typename V, typename E, typename G>

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

pure virtual

Implemented in core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >, core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >, and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::BackgroundNode< V, E, G >::drop_edge ( BackgroundEdgeListIter edge )

removes an edge from the nodes edge list in constant time

Remarks: Invalidates edge_vector_up_to_date_ flag

Parameters

edge	- [in] - the iterator to the edge's position in node's edge list

template<typename V , typename E , typename G >

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

Linear time edge lookup function.

Parameters

fc_node_index - [in] - the index of the first class node that is on the other end of the sought edge

template<typename V, typename E, typename G>

FirstClassNode< V, E, G>* core::pack::interaction_graph::BackgroundNode< V, E, G >::get_adjacent_first_class_node ( int index ) const

inlineprotected

References core::pack::interaction_graph::BackgroundNode< V, E, G >::adjacent_nodes_, and core::pack::interaction_graph::BackgroundNode< V, E, G >::edge_vector_up_to_date_.

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::BackgroundNode< V, E, G >::get_edge_vector_up_to_date ( ) const

inlineprotected

References core::pack::interaction_graph::BackgroundNode< V, E, G >::edge_vector_up_to_date_.

template<typename V, typename E, typename G>

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

inlineprotected

References core::pack::interaction_graph::BackgroundNode< V, E, G >::edge_vector_, and core::pack::interaction_graph::BackgroundNode< V, E, G >::edge_vector_up_to_date_.

Referenced by core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_bg_edge(), core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_npd_hbond_bg_edge(), and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::get_surface_bg_edge().

template<typename V, typename E, typename G>

int core::pack::interaction_graph::BackgroundNode< V, E, G >::get_index_of_adjacent_first_class_node ( int index ) const

inlineprotected

References core::pack::interaction_graph::BackgroundNode< V, E, G >::adjacent_first_class_node_indices_, and core::pack::interaction_graph::BackgroundNode< V, E, G >::edge_vector_up_to_date_.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::BackgroundNode< V, E, G >::get_node_index ( ) const

inlineprotected

References core::pack::interaction_graph::BackgroundNode< V, E, G >::node_index_.

Referenced by core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::wt_residue_for_node().

template<typename V, typename E, typename G>

int core::pack::interaction_graph::BackgroundNode< V, E, G >::get_num_incident_edges ( ) const

inlineprotected

References core::pack::interaction_graph::BackgroundNode< V, E, G >::num_incident_edges_.

template<typename V, typename E, typename G>

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

inlineprotected

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

Referenced by core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_owner(), core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_npd_hbond_owner(), and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::get_surface_owner().

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

pure virtual

Implemented in core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >, core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >, and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >.

template<typename V, typename E, typename G>

virtual void core::pack::interaction_graph::BackgroundNode< V, E, G >::print ( ) const

pure virtual

Implemented in core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >, core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >, and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::BackgroundNode< V, E, G >::update_edge_vector ( )

protected

Syncs the edge vector with the edge list.

Updates the vector of pointers to background edges to correspond to the list of background edges. Informs its incident edges of their position in its vector.