Defines a Surface edge which will be used in determining surface energy. More...

#include <SurfaceInteractionGraph.hh>

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

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

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

Public Member Functions
	SurfaceEdge (G *owner, int node1, int node2)
	main constructor. No default, or copy constructors, no assignment operator More...

virtual	~SurfaceEdge ()

void	acknowledge_state_zeroed_surface (int node_index)
	respond to when one of its vertices enters the "unassigned" state More...

Real	get_surface_deltaE_for_neighbor (int node_considering_substitution, int alt_state)
	returns the change in surface score for the neighbor of a node that is produced by the state substitution it is considering. More...

Real	get_current_two_body_energy () const

void	acknowledge_substitution_surface ()
	bookkeeping following the decision to substitute a nodes current state with the alternate it was asked to consider. More...

virtual void	declare_energies_final ()
	Reduces memory usage in the two body energy table after the energy calculating function declares that the energies will not change thereafter. More...

virtual void	prepare_for_simulated_annealing ()
	drops zero submatrices of the AminoAcidNeighborSparseMatrix and if the two_body_energies_ member then holds nothing, it checks whether or not its incident nodes have any sphere overlaps. If they don't then the edge deletes itself. More...

virtual unsigned int	getMemoryUsageInBytes () const

Real	get_max_surface_deltaE_guess (int node_changing) const

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 (int index)

Public Member Functions inherited from core::pack::interaction_graph::FirstClassEdge< V, E, G >
virtual	~FirstClassEdge ()
	FirstClassEdge destructor. More...

	FirstClassEdge (G *owner, int first_node_ind, int second_node_ind)
	FirstClassEdge constructor. More...

Private Member Functions
void	inform_non_changing_node_of_neighbors_change ()
	tells the node that isn't considering a substitution or changing state that its neighbor who is has changed. More...

void	track_max_magnitude_surface_deltaE ()
	Keeps track of the maximum surface deltaE seen in the last 50 commits. More...

	SurfaceEdge ()

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

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

Private Attributes
int	node_changing_

int	node_not_changing_

int	nodes_curr_states_ [2]

int	nodes_alt_states_ [2]

Real	max_surface_deltaE_last_50_commits_ [2]

Real	max_surface_deltaE_recent_50_commits_ [2]

Real	magnitude_last_surface_deltaE_ [2]

int	num_surface_deltaE_observations_since_update_ [2]

Detailed Description

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

Defines a Surface edge which will be used in determining surface energy.

SurfaceEdge

Definition at line 63 of file SurfaceInteractionGraph.hh.

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef FirstClassEdge< V, E, G > core::pack::interaction_graph::SurfaceEdge< V, E, G >::parent

Definition at line 335 of file SurfaceInteractionGraph.hh.

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

core::pack::interaction_graph::SurfaceEdge< V, E, G >::SurfaceEdge	(	G *	owner,
		int	node1,
		int	node2
	)

main constructor. No default, or copy constructors, no assignment operator

SurfaceEdge::SurfaceEdge

Parameters

owner - [in] - the owning interaction graph object node1 - [in] - the index of the lower-indexed SurfaceNode node2 - [in] - the index of the higher-indexed SurfaceNode

Definition at line 2726 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceEdge< V, E, G >::magnitude_last_surface_deltaE_, core::pack::interaction_graph::SurfaceEdge< V, E, G >::max_surface_deltaE_last_50_commits_, core::pack::interaction_graph::SurfaceEdge< V, E, G >::max_surface_deltaE_recent_50_commits_, core::pack::interaction_graph::SurfaceEdge< V, E, G >::nodes_alt_states_, core::pack::interaction_graph::SurfaceEdge< V, E, G >::nodes_curr_states_, and core::pack::interaction_graph::SurfaceEdge< V, E, G >::num_surface_deltaE_observations_since_update_.

template<typename V , typename E , typename G >

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

virtual

SurfaceEdge::~SurfaceEdge

Definition at line 2748 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceEdge< V, E, G >::acknowledge_state_zeroed_surface ( int node_that_changed)

respond to when one of its vertices enters the "unassigned" state

SurfaceEdge::acknowledge_state_zeroed_surface

Parameters

node_that_changed - [in] - the index of the node that changed

Definition at line 2789 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

bookkeeping following the decision to substitute a nodes current state with the alternate it was asked to consider.

SurfaceEdge::acknowledge_substitution_surface

Definition at line 2849 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

SurfaceEdge::count_dynamic_memory

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

Definition at line 2959 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

SurfaceEdge::count_static_memory

Definition at line 2950 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceEdge< V, E, G >::declare_energies_final ( )

virtual

Reduces memory usage in the two body energy table after the energy calculating function declares that the energies will not change thereafter.

SurfaceEdge::declare_energies_final

Remarks: (all by apl) In the PDEdge's version of this method, after invoking two_body_energies_.drop_zero_submatrices_where_possible(); the PDEdge checks if the two body energy table it now holds is empty. If the table is empty, the edge deletes itself.

A SASAEdge should not delete itself if the pair energies are all zero since the Minkowski sum of a water and a van der Waal's sphere extends further out from an atoms center than its (lj_atr, lj_rep, lksolv) interaction sphere. However, if a SASAEdge holds no pair energies, it's a very good candidate for removal – it just first needs to check that no (vdw + 1.4 A) spheres overlap between any pair of rotamers on the edges it connects.

Definition at line 2920 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceEdge< V, E, G >::get_current_two_body_energy ( ) const

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceEdge< V, E, G >::get_max_surface_deltaE_guess ( int node_changing) const

SurfaceEdge::get_max_surface_deltaE_guess

Definition at line 2929 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceEdge< V, E, G >::get_surface_deltaE_for_neighbor	(	int	node_considering_substitution,
		int	alt_state
	)

returns the change in surface score for the neighbor of a node that is produced by the state substitution it is considering.

SurfaceEdge::get_surface_deltaE_for_neighbor

Detailed:: Need to tell the node that's not changing which node is considering the change and what the alternate state it might change to is. Then that node can recompute it's change in se hp nb count and return a change in score.

Definition at line 2813 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

SurfaceNode< V, E, G >* core::pack::interaction_graph::SurfaceEdge< V, E, G >::get_surface_node ( int index)

inline

Definition at line 370 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::SurfaceEdge< V, E, G >::getMemoryUsageInBytes ( ) const

virtual

SurfaceEdge::getMemoryUsageInBytes

Remarks: Not implemented.

Definition at line 2941 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceEdge< V, E, G >::inform_non_changing_node_of_neighbors_change ( )

inlineprivate

tells the node that isn't considering a substitution or changing state that its neighbor who is has changed.

SurfaceEdge::inform_non_changing_node_of_neighbors_change

Definition at line 2869 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

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

private

template<typename V , typename E , typename G >

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

virtual

drops zero submatrices of the AminoAcidNeighborSparseMatrix and if the two_body_energies_ member then holds nothing, it checks whether or not its incident nodes have any sphere overlaps. If they don't then the edge deletes itself.

SurfaceEdge::prepare_for_simulated_annealing

Definition at line 2759 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

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

inline

Definition at line 360 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

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

private

Keeps track of the maximum surface deltaE seen in the last 50 commits.

SurfaceEdge::track_max_magnitude_surface_deltaE