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

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 >:

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...
	~SurfaceBackgroundEdge () override
void	prepare_for_simulated_annealing () override
	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...
unsigned int	count_static_memory () const override
unsigned int	count_dynamic_memory () const override
	Returns an int representing the amount of memory in bytes used by this node. More...
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...
bool	bgtfce_marked_for_deletion ()

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
void	bgtfce_mark_edge_for_deletion ()

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)

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

Member Typedef Documentation

template<typename V, typename E, typename G>

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

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

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

template<typename V , typename E , typename G >

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

override

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).

Parameters

new_state

- [in] - the state the SurfaceNode switched to

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

template<typename V , typename E , typename G >

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

overridevirtual

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

Remarks

return 0 because no memory is dynamically allocated for these edges.

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

template<typename V , typename E , typename G >

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

overridevirtual

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

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_.

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

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

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

template<typename V, typename E, typename G>

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

inline

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 ( )

overridevirtual

Invoked by AdditionalBackgroundNodesInteractionGraph::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 >.

template<typename V, typename E, typename G>

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

inline

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.

Member Data Documentation

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

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

template<typename V, typename E, typename G>

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

private

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

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