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 >:

Collaboration 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.

BackgroundNode

Detailed:: 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().

Definition at line 36 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 178 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

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

Definition at line 177 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

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

Definition at line 179 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

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

Definition at line 180 of file AdditionalBackgroundNodesInteractionGraph.hh.

template<typename V, typename E, typename G>

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

Definition at line 181 of file AdditionalBackgroundNodesInteractionGraph.hh.

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

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

virtual

BackgroundNode destructor.

BackgroundNode::~BackgroundNode

Definition at line 632 of file AdditionalBackgroundNodesInteractionGraph.hh.

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 =.

BackgroundNode::BackgroundNode

Detailed:: 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

Definition at line 618 of file AdditionalBackgroundNodesInteractionGraph.hh.

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.

BackgroundNode::add_edge

Remarks: Invalidates edge_vector_up_to_date_ flag

Parameters

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

Definition at line 648 of file AdditionalBackgroundNodesInteractionGraph.hh.

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.

BackgroundNode::count_dynamic_memory

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 >, and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >.

Definition at line 745 of file AdditionalBackgroundNodesInteractionGraph.hh.

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 >, 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

BackgroundNode::drop_edge

Remarks: Invalidates edge_vector_up_to_date_ flag

Parameters

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

Definition at line 667 of file AdditionalBackgroundNodesInteractionGraph.hh.

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.

BackgroundNode::find_edge

Parameters

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

Definition at line 721 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 218 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 224 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 206 of file AdditionalBackgroundNodesInteractionGraph.hh.

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(), 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

Definition at line 212 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 200 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 203 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Definition at line 227 of file AdditionalBackgroundNodesInteractionGraph.hh.

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

Referenced by core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_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 >, 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 >, 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.

BackgroundNode::update_edge_vector

Detailed:: 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.