Function declarations for the AdditionalBackgroundNodesInteractionGraph. More...

#include <AdditionalBackgroundNodesInteractionGraph.hh>

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

[legend]

Public Types
typedef std::vector< BackgroundNode< V, E, G > * >	BackgroundNodeVector

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

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

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

Public Member Functions
	AdditionalBackgroundNodesInteractionGraph (int num_nodes)
	AdditionalBackgroundNodesInteractionGraph constructor; no default or copy constructors; no operator =. More...

	~AdditionalBackgroundNodesInteractionGraph () override
	AdditionalBackgroundNodesInteractionGraph destructor. More...

unsigned int	getTotalMemoryUsage () const override
	Returns an int representing the total amount of memory in bytes used by this graph. More...

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

int	get_num_background_nodes () const

Protected Member Functions
void	clean_up_bgtfc_edges_marked_for_deletion ()
	Remove those BackgroundToFirstClassEdges that have marked themselves for deletion. More...

void	drop_background_edge (BackgroundEdgeListIter iter)
	Constant time edge removal. More...

virtual BackgroundNode< V, E, G > *	create_background_node (int bg_node_index)=0

virtual BackgroundToFirstClassEdge< V, E, G > *	create_background_edge (int fc_node_index, int bg_node_index)=0

void	set_num_background_nodes (int num_bg_nodes)
	sets the number of background nodes in the graph. Should be called no more than once. Some problem instances do not require background nodes. More...

void	add_background_edge (int first_class_node_index, int bg_node_index)
	adds a BackgroundToFirstClassEdge to the graph and performs the requisite bookkeepking. More...

BackgroundToFirstClassEdge< V, E, G > *	find_background_edge (int first_class_node_index, int bg_node_index) const
	returns a pointer to the background edge, identified by the indices of the first and second class nodes it connects. Returns the null pointer if the edge does not exist. Possibly linear time operation (in the number of BackgroundToFirstClassEdges). More...

int	get_num_bg_edges () const

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

void	prepare_graph_for_simulated_annealing () override
	invokes prepare_for_simulated_annealing on each of the BackgroundToFirstClassEdges and then invokes prepare_for_simulated_annealing on each of the BackgroundNodes. More...

BackgroundEdgeListConstIter	get_bg_edge_list_begin () const

BackgroundEdgeListConstIter	get_bg_edge_list_end () const

Private Member Functions
	AdditionalBackgroundNodesInteractionGraph ()

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

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

Private Attributes
int	num_bg_nodes_

BackgroundNodeVector	bg_nodes_

BackgroundEdgeList	bg_to_fc_edge_list_

BackgroundToFirstClassEdge< V, E, G > *	focused_bg_edge_

Friends
class	BackgroundToFirstClassEdge< V, E, G >

Detailed Description

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

Function declarations for the AdditionalBackgroundNodesInteractionGraph.

Member Typedef Documentation

◆ BackgroundEdgeList

template<typename V , typename E , typename G >

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

◆ BackgroundEdgeListConstIter

template<typename V , typename E , typename G >

typedef std::list< BackgroundToFirstClassEdge< V, E, G > * >::const_iterator core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::BackgroundEdgeListConstIter

◆ BackgroundEdgeListIter

template<typename V , typename E , typename G >

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

◆ BackgroundNodeVector

template<typename V , typename E , typename G >

typedef std::vector< BackgroundNode< V, E, G > * > core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::BackgroundNodeVector

Constructor & Destructor Documentation

◆ AdditionalBackgroundNodesInteractionGraph() [1/3]

template<typename V , typename E , typename G >

core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::AdditionalBackgroundNodesInteractionGraph ( int num_nodes )

AdditionalBackgroundNodesInteractionGraph constructor; no default or copy constructors; no operator =.

Parameters

num_nodes - [in] - the number of first class nodes

◆ ~AdditionalBackgroundNodesInteractionGraph()

template<typename V , typename E , typename G >

core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::~AdditionalBackgroundNodesInteractionGraph

override

AdditionalBackgroundNodesInteractionGraph destructor.

deallocates each BackgroundToFirstClassEdge. Then deallocates each background node. Order is important. The edges assume that its vertices still exist at the time it is removed. This destructor enforces that.

◆ AdditionalBackgroundNodesInteractionGraph() [2/3]

template<typename V , typename E , typename G >

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

private

◆ AdditionalBackgroundNodesInteractionGraph() [3/3]

template<typename V , typename E , typename G >

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

private

Member Function Documentation

◆ add_background_edge()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::add_background_edge	(	int	first_class_node_index,
		int	bg_node_index
	)

protected

adds a BackgroundToFirstClassEdge to the graph and performs the requisite bookkeepking.

Parameters

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

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

◆ clean_up_bgtfc_edges_marked_for_deletion()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::clean_up_bgtfc_edges_marked_for_deletion

protected

Remove those BackgroundToFirstClassEdges that have marked themselves for deletion.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.irio.nosp@m.ninst.nosp@m.itut.nosp@m.e.org).

◆ count_dynamic_memory()

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::count_dynamic_memory

override

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

◆ create_background_edge()

template<typename V , typename E , typename G >

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

protectedpure virtual

Implemented in core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >, core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >, and core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >.

◆ create_background_node()

template<typename V , typename E , typename G >

virtual BackgroundNode< V, E, G >* core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::create_background_node ( int bg_node_index )

protectedpure virtual

Implemented in core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >, core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >, and core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >.

◆ drop_background_edge()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::drop_background_edge ( BackgroundEdgeListIter iter )

protected

Constant time edge removal.

Parameters

iter	- [in] - the iterator to the position in the graph's edge list for the edge that is removing itself.

◆ find_background_edge()

template<typename V , typename E , typename G >

BackgroundToFirstClassEdge< V, E, G > * core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::find_background_edge	(	int	first_class_node_index,
		int	bg_node_index
	)		const

protected

returns a pointer to the background edge, identified by the indices of the first and second class nodes it connects. Returns the null pointer if the edge does not exist. Possibly linear time operation (in the number of BackgroundToFirstClassEdges).

The graph keeps a pointer to a "focused edge" so that repeated requests for the same edge take constant time.

Parameters

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

◆ get_background_node()

template<typename V , typename E , typename G >

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

inlineprotected

References core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::bg_nodes_, and core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::num_bg_nodes_.

Referenced by core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::get_hpatch_bg_node(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_npd_hbond_bg_node(), and core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::get_surface_bg_node().

◆ get_bg_edge_list_begin()

template<typename V , typename E , typename G >

BackgroundEdgeListConstIter core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_bg_edge_list_begin ( ) const

inlineprotected

References core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::bg_to_fc_edge_list_.

◆ get_bg_edge_list_end()

template<typename V , typename E , typename G >

BackgroundEdgeListConstIter core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_bg_edge_list_end ( ) const

inlineprotected

References core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::bg_to_fc_edge_list_.

◆ get_num_background_nodes()

template<typename V , typename E , typename G >

int core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_num_background_nodes ( ) const

inline

References core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::num_bg_nodes_.

◆ get_num_bg_edges()

template<typename V , typename E , typename G >

int core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_num_bg_edges ( ) const

inlineprotected

References core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::bg_to_fc_edge_list_.

◆ getTotalMemoryUsage()

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::getTotalMemoryUsage

override

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

◆ operator=()

template<typename V , typename E , typename G >

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

private

◆ prepare_graph_for_simulated_annealing()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::prepare_graph_for_simulated_annealing

overrideprotected

invokes prepare_for_simulated_annealing on each of the BackgroundToFirstClassEdges and then invokes prepare_for_simulated_annealing on each of the BackgroundNodes.

A BackgroundToFirstClassEdges may decide to delete itself before sim annealing begins. Since the second class node will likely update is edge vector in its (virtual) call to prepare_for_sim_annealing, any edges that should be should be removed before the second class nodes update their edge vectors.

Remarks: does not invoke InteractionGraphBase::prepare_graph_for_simulated_annealing()

◆ set_num_background_nodes()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::set_num_background_nodes ( int num_bg_nodes )

protected

sets the number of background nodes in the graph. Should be called no more than once. Some problem instances do not require background nodes.

Allocates the background nodes using a factory method. Their indices start from 1. The create_background_node() method is virtual.

Friends And Related Function Documentation

◆ BackgroundToFirstClassEdge< V, E, G >

template<typename V , typename E , typename G >

friend class BackgroundToFirstClassEdge< V, E, G >

friend

Member Data Documentation

◆ bg_nodes_

template<typename V , typename E , typename G >

BackgroundNodeVector core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::bg_nodes_

private

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

◆ bg_to_fc_edge_list_

template<typename V , typename E , typename G >

BackgroundEdgeList core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::bg_to_fc_edge_list_

private

Referenced by core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_bg_edge_list_begin(), core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_bg_edge_list_end(), and core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_num_bg_edges().

◆ focused_bg_edge_

template<typename V , typename E , typename G >

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

mutableprivate

◆ num_bg_nodes_

template<typename V , typename E , typename G >

int core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::num_bg_nodes_

private

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

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

src/core/pack/interaction_graph/AdditionalBackgroundNodesInteractionGraph.hh

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

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

Member Typedef Documentation

◆ BackgroundEdgeList

◆ BackgroundEdgeListConstIter

◆ BackgroundEdgeListIter

◆ BackgroundNodeVector

Constructor & Destructor Documentation

◆ AdditionalBackgroundNodesInteractionGraph() [1/3]

◆ ~AdditionalBackgroundNodesInteractionGraph()

◆ AdditionalBackgroundNodesInteractionGraph() [2/3]

◆ AdditionalBackgroundNodesInteractionGraph() [3/3]

Member Function Documentation

◆ add_background_edge()

◆ clean_up_bgtfc_edges_marked_for_deletion()

◆ count_dynamic_memory()

◆ create_background_edge()

◆ create_background_node()

◆ drop_background_edge()

◆ find_background_edge()

◆ get_background_node()

◆ get_bg_edge_list_begin()

◆ get_bg_edge_list_end()

◆ get_num_background_nodes()

◆ get_num_bg_edges()

◆ getTotalMemoryUsage()

◆ operator=()

◆ prepare_graph_for_simulated_annealing()

◆ set_num_background_nodes()

Friends And Related Function Documentation

◆ BackgroundToFirstClassEdge< V, E, G >

Member Data Documentation

◆ bg_nodes_

◆ bg_to_fc_edge_list_

◆ focused_bg_edge_

◆ num_bg_nodes_

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