Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode) More...

#include <HPatchInteractionGraph.hh>

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
	HPatchBackgroundEdge (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int first_class_node_index, int background_node_index)
	main constructor More...

virtual	~HPatchBackgroundEdge ()

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

void	initialize_overlap_cache (RotamerDots const &bg_residue)
	compute the sphere overlaps of the background node with every state on the first class node. The HPatchBackgroundEdge hands its stl vector of RotamerDotsCache objects (node_states_coverage_of_bg_res) to the HPatchNode More...

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

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

void	acknowledge_substitution ()
	bookkeeping in response to the HPatchNode committing the considered substitution More...

utility::vector1 < utility::vector1< bool > > const &	get_atom_atom_overlaps_for_state (Size state) const
	Returns a const reference to the atom-x-atom-pair vector-of-vectors of bools that specifies which atoms are overlapping, assuming the alternate state assignment. More...

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () 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...

Protected Member Functions
HPatchNode< V, E, G > *	get_hpatch_node () const

HPatchBackgroundNode< V, E, G > *	get_hpatch_bg_node () const

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

Private Member Functions
	HPatchBackgroundEdge ()

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

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

Private Attributes
bool	prepared_for_simA_

Size	bg_res_num_atoms_

std::vector< RotamerDotsCache >	node_states_coverage_of_bg_res_

int	nodes_curr_state_

int	nodes_alt_state_

RotamerDotsCache	curr_dots_cache_

RotamerDotsCache	alt_dots_cache_

std::vector< utility::vector1 < utility::vector1< bool > > >	node_states_overlap_with_bg_res_

utility::vector1< std::pair < Size, Size > >	curr_state_exolap_hphobes_
	pairs of hphobes that have exposed overlap More...

utility::vector1< std::pair < Size, Size > >	alt_state_exolap_hphobes_

Detailed Description

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

Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode)

HPatchBackgroundEdge

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

Member Typedef Documentation

template<typename V, typename E, typename G>

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

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

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

main constructor

HPatchBackgroundEdge< V, E, G >::HPatchBackgroundEdge

template<typename V , typename E , typename G >

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

virtual

HPatchBackgroundEdge::~HPatchBackgroundEdge

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

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

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

HPatchBackgroundEdge::acknowledge_state_change

Detailed:: State "0" is handled by the HPatchBackgroundEdge just like any other state. The dot overlap cache is simply empty: the unassigned state induces no overlap on the background node. The HPatchBackgroundEdge keeps a stl vector of RotamerDotCaches. Position 0 in that vector holds a Cache object of nothing but 0's.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::acknowledge_substitution ( )

bookkeeping in response to the HPatchNode committing the considered substitution

HPatchBackgroundEdge::acknowledge_substitution

template<typename V , typename E , typename G >

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

virtual

HPatchBackgroundEdge::count_dynamic_memory

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

template<typename V , typename E , typename G >

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

virtual

HPatchBackgroundEdge::count_static_memory

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

template<typename V , typename E , typename G >

utility::vector1< utility::vector1< bool > > const & core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::get_atom_atom_overlaps_for_state ( Size state ) const

Returns a const reference to the atom-x-atom-pair vector-of-vectors of bools that specifies which atoms are overlapping, assuming the alternate state assignment.

HPatchBackgroundEdge< V, E, G >::get_atom_atom_self_overlaps_for_state

template<typename V, typename E, typename G>

HPatchBackgroundNode< V, E, G >* core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::get_hpatch_bg_node ( ) const

inlineprotected

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

template<typename V, typename E, typename G>

HPatchNode< V, E, G >* core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::get_hpatch_node ( ) const

inlineprotected

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::initialize_overlap_cache ( RotamerDots const & bg_residue_dots )

compute the sphere overlaps of the background node with every state on the first class node. The HPatchBackgroundEdge hands its stl vector of RotamerDotsCache objects (node_states_coverage_of_bg_res) to the HPatchNode

HPatchBackgroundEdge::initialize_overlap_cache

Called during the prep for simA method in HPatchBGNodes. This method in turn calls a HPatchNode method, init_overlap_with_background to set the vector of RDC object pointers.

References core::pack::interaction_graph::RotamerDots::get_num_atoms().

template<typename V, typename E, typename G>

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

private

template<typename V , typename E , typename G >

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

virtual

Invoked by AdditionalBackgroundNodesInteractionGraph::prepare_for_simulated_annealing.

HPatchBackgroundEdge::prepare_for_simulated_annealing

Remarks: The HPatchBackgroundEdge has no responsibilities in this function. However, when the AdditionalBackgroundNodesInteractionGraph invokes prepare_for_simulated_annealing on the HPatchBackgroundNode 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 >

Real core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::update_state_at_neighbor ( int alt_state )

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

HPatchBackgroundEdge::update_state_at_neighbor

Member Data Documentation

template<typename V, typename E, typename G>

RotamerDotsCache core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::alt_dots_cache_

private

template<typename V, typename E, typename G>

utility::vector1< std::pair< Size, Size > > core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::alt_state_exolap_hphobes_

private

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::bg_res_num_atoms_

private

template<typename V, typename E, typename G>

RotamerDotsCache core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::curr_dots_cache_

private

template<typename V, typename E, typename G>

utility::vector1< std::pair< Size, Size > > core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::curr_state_exolap_hphobes_

private

pairs of hphobes that have exposed overlap

template<typename V, typename E, typename G>

std::vector< RotamerDotsCache > core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::node_states_coverage_of_bg_res_

private

template<typename V, typename E, typename G>

std::vector< utility::vector1< utility::vector1< bool > > > core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::node_states_overlap_with_bg_res_

private

template<typename V, typename E, typename G>

int core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::nodes_alt_state_

private

template<typename V, typename E, typename G>

int core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::nodes_curr_state_

private

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::prepared_for_simA_

private

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

src/core/pack/interaction_graph/HPatchInteractionGraph.hh

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

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