Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode) More...

#include <SurfaceInteractionGraph.hh>

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

Collaboration diagram for core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >:

Public Types
typedef BackgroundToFirstClassEdge< V, E, G >	parent

Public Types inherited from core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >::iterator	BackgroundEdgeListIter

Public Member Functions
	SurfaceBackgroundEdge (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int first_class_node_index, int background_node_index)
	main constructor More...

virtual	~SurfaceBackgroundEdge ()

void	prepare_for_simulated_annealing ()
	Invoked by AdditionalBackgroundNodesInteractionGraph::prepare_for_simulated_annealing. More...

Real	get_surface_deltaE_for_substitution (int alt_state)
	returns the change in surface energy produced by a background node in response to a considered state substitution of the first class node More...

void	acknowledge_substitution_surface ()
	bookkeeping in response to the SurfaceNode committing the considered substitution More...

void	acknowledge_state_change (int new_state)
	bookkeeping in response to a SurfaceNode switching states (without having gone through the usual consider-substitution/commit-substitution pattern). More...

Real	get_max_surface_deltaE_guess () const
	Returns the value of max_surface_deltaE_last_50_commits_. More...

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

void	set_max_surface_deltaE ()

SurfaceNode< V, E, G > *	get_surface_node () const

SurfaceBackgroundNode< V, E, G > *	get_surface_bg_node () const

Public Member Functions inherited from core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
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...

Private Member Functions
void	track_max_magnitude_surface_deltaE ()
	Keeps track of the maximum surface deltaE seen in the last 50 commits. Used possibly for procrastinating recalculations of the surface score. More...

	SurfaceBackgroundEdge ()

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

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

Private Attributes
int	fc_node_curr_state_

int	fc_node_alt_state_

Real	max_surface_deltaE_last_50_commits_

Real	max_surface_deltaE_recent_50_commits_

Real	magnitude_last_surface_deltaE_

int	num_surface_deltaE_observations_since_update_

Additional Inherited Members
Protected Member Functions inherited from core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
FirstClassNode< V, E, G > *	get_first_class_node () const

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

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

Detailed Description

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

Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode)

SurfaceBackgroundEdge

Detailed:: In addition to implementing the virtual base class methods, this class additionally defines methods relating to keeping track of data relating to surface.

Definition at line 64 of file SurfaceInteractionGraph.hh.

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef BackgroundToFirstClassEdge< V, E, G > core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::parent

Definition at line 416 of file SurfaceInteractionGraph.hh.

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::SurfaceBackgroundEdge	(	AdditionalBackgroundNodesInteractionGraph< V, E, G > *	owner,
		int	first_class_node_index,
		int	background_node_index
	)

main constructor

SurfaceBackgroundEdge< V, E, G >::SurfaceBackgroundEdge

Parameters

owner - [in] - the owning graph first_class_node_index - [in] - the index of the first class node upon which this new edge is incident second_class_node_index - [in] - the index of the second class node upon which this new edge is incident

Definition at line 2986 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

SurfaceBackgroundEdge::~SurfaceBackgroundEdge

Definition at line 3004 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::acknowledge_state_change ( int new_state)

bookkeeping in response to a SurfaceNode switching states (without having gone through the usual consider-substitution/commit-substitution pattern).

SurfaceBackgroundEdge::acknowledge_state_change

Parameters

new_state - [in] - the state the SurfaceNode switched to

Definition at line 3035 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::acknowledge_substitution_surface ( )

bookkeeping in response to the SurfaceNode committing the considered substitution

SurfaceBackgroundEdge::acknowledge_substitution_surface

Definition at line 3089 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

SurfaceBackgroundEdge::count_dynamic_memory

Reimplemented from core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >.

Definition at line 3148 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

SurfaceBackgroundEdge::count_static_memory

Implements core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >.

Definition at line 3139 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::get_max_surface_deltaE_guess ( ) const

Returns the value of max_surface_deltaE_last_50_commits_.

SurfaceBackgroundEdge::get_max_surface_deltaE_guess

Definition at line 3130 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

SurfaceBackgroundNode< V, E, G >* core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::get_surface_bg_node ( ) const

inline

Definition at line 450 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::get_surface_deltaE_for_substitution ( int alt_state)

returns the change in surface energy produced by a background node in response to a considered state substitution of the first class node

SurfaceBackgroundEdge::get_surface_deltaE_for_substitution

Detailed:: Need to tell the bg node that's not changing that the fc node is considering a change and what the alternate state it might change to is. Then that node can recompute it's change in se hp nb total hASA and return a change in score. Called once by acknowledge_state_change method in this class when blanket setting the state of all the nodes to zero during initialization.

Parameters

alt_state - [in] - the alternate state (i.e. rotamer id) that the first class node is considering

Definition at line 3062 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

SurfaceNode< V, E, G >* core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::get_surface_node ( ) const

inline

Definition at line 441 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

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

private

template<typename V , typename E , typename G >

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

virtual

Invoked by AdditionalBackgroundNodesInteractionGraph::prepare_for_simulated_annealing.

SurfaceBackgroundEdge::prepare_for_simulated_annealing

Remarks: The SurfaceBackgroundEdge has no responsibilities in this function. However, when the AdditionalBackgroundNodesInteractionGraph invokes prepare_for_simulated_annealing on the SurfaceBackgroundNode that this edge is incident upon, that node will invoke initialize_overlap_cache on this edge

Implements core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >.

Definition at line 3021 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

void core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::set_max_surface_deltaE ( )

inline

Definition at line 434 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::max_surface_deltaE_last_50_commits_.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::track_max_magnitude_surface_deltaE ( )

private

Keeps track of the maximum surface deltaE seen in the last 50 commits. Used possibly for procrastinating recalculations of the surface score.

SurfaceBackgroundEdge::track_max_magnitude_surface_deltaE

Definition at line 3107 of file SurfaceInteractionGraph.hh.

Member Data Documentation

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::fc_node_alt_state_

private

Definition at line 456 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::fc_node_curr_state_

private

Definition at line 455 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::magnitude_last_surface_deltaE_

private

Definition at line 460 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::max_surface_deltaE_last_50_commits_

private

Definition at line 458 of file SurfaceInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::set_max_surface_deltaE().

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::max_surface_deltaE_recent_50_commits_

private

Definition at line 459 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >::num_surface_deltaE_observations_since_update_

private

Definition at line 461 of file SurfaceInteractionGraph.hh.

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

src/core/pack/interaction_graph/SurfaceInteractionGraph.hh

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

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

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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