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

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 >:

List of all members.

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.
	BackgroundNode (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int node_index)
	BackgroundNode constructor - no default or copy constructors; no operator =.
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.
void	drop_edge (BackgroundEdgeListIter edge)
	removes an edge from the nodes edge list in constant time
BackgroundToFirstClassEdge< V, E, G > *	find_edge (int fc_node_index)
	Linear time edge lookup function.
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.
Protected Member Functions
void	update_edge_vector ()
	Syncs the edge vector with the edge list.
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

---

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().

---

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.

BackgroundNode::~BackgroundNode

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

---

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

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 >.

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

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

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 [inline, protected]

template<typename V, typename E, typename G>

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

(

)

const [inline, protected]

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 [inline, protected]

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 [inline, protected]

template<typename V, typename E, typename G>

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

(

)

const [inline, protected]

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 [inline, protected]

template<typename V, typename E, typename G>

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

(

)

const [inline, protected]

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>

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.

Remarks:

sets edge_vector_up_to_date_ flag to true

---

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

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