#include <DoubleDensePDInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::DoubleDensePDEdge:

Public Member Functions
	DoubleDensePDEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
	main constructor - no default nor copy constructors provided More...

	~DoubleDensePDEdge () override
	destructor. All dynamically allocated memory is managed by the objects contained inside the DoubleDensePDEdge, so there is no work to be (explicitly) done. More...

void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &) override

bool	get_sparse_aa_info (int, int) const override

void	add_to_two_body_energy (int const, int const, core::PackerEnergy const) override
	adds the input energy to the two body energy for state1 on the node with the smaller index and state2 on the node with the larger index. More...

void	add_to_two_body_energies (ObjexxFCL::FArray2< core::PackerEnergy > const &res_res_energy_array) override
	Adds all the energies stored in the oversized_res_res_energy array to the two body energy table for those states whose amion acid types were previoudsly declared to be amino-acid neighbors. The res-res array should have the dimension (node1->get_num_states() x node2->get_num_states());. More...

void	set_two_body_energy (int const, int const, core::PackerEnergy const) override
	Sets the two-body energy for a pair of states. That is, it overwrites whatever two-body energy there was previously for that state pair with a new energy. Ignores non-neighboring state pairs. More...

void	clear_two_body_energy (int const, int const) override
	Sets the two-body energy for a pair of states. That is, it overwrites whatever two-body energy there was previously for that state pair with a new energy. Ignores non-neighboring state pairs. More...

core::PackerEnergy	get_two_body_energy (int const, int const ) const override
	returns the two body energy for a pair of states: 0 if those states are not neighbors More...

void	force_aa_neighbors (int, int) override

void	force_all_aa_neighbors () override

void	declare_energies_final () override
	If all of the energies for an edge have been added in, then declare the edge energies final. This may mean that the edge deletes itself. More...

void	prepare_for_simulated_annealing () override
	looks at all pair energies, and if they are all 0, deletes itself More...

core::PackerEnergy	get_current_two_body_energy ()
	returns the two body energy corresponding to the current states assigned to the nodes this edge is incident upon. More...

void	acknowledge_state_change (int node_ind, int new_state, core::PackerEnergy &new_energy)
	updates bookkeeping information when one of the two nodes changes its state More...

void	acknowledge_state_zeroed (int node_ind)
	updates bookkeeping information when one of the two nodes enters its "unassigned" state. More...

void	acknowledge_substitution (int substituted_node_index, core::PackerEnergy const curr_state_energy, int nodes_new_state)
	update bookkeeping information when one of the nodes an edge is incident upon changes state More...

int	get_two_body_table_size () const
	Returns a reference to the first element in the dense two-body energy table. Used to create a proxy array on the nodes for cache efficiency. More...

unsigned int	count_static_memory () const override
	returns sizeof DoubleDensePDEdge if this is the most-derived instance of the class More...

unsigned int	count_dynamic_memory () const override
	returns the amount of memory dynamically allocated by the edge and recurses on its parent (in this case, the EdgeBase class) More...

void	set_edge_weight (Real weight) override

Public Member Functions inherited from core::pack::interaction_graph::PrecomputedPairEnergiesEdge
	~PrecomputedPairEnergiesEdge () override

	PrecomputedPairEnergiesEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)

Public Member Functions inherited from core::pack::interaction_graph::FixedBBEdge
	~FixedBBEdge () override

	FixedBBEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)

Public Member Functions inherited from core::pack::interaction_graph::EdgeBase
virtual	~EdgeBase ()
	copy constructor, do not use More...

	EdgeBase (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
	main constructor for edge, no default nor copy constructors More...

int	get_other_ind (int callers_index) const
	returns the index of the other node that the edge is incident upon More...

NodeBase *	get_other_node (int callers_index) const
	returns a pointer to the other node that the edge is incident upon More...

int	get_first_node_ind () const
	returns the index of the smaller-indexed node More...

int	get_second_node_ind () const
	returns the index of the larger-indexed node More...

void	set_pos_in_owners_list (std::list< EdgeBase * >::iterator edge_iterator)
	edge keeps iterator to its position in it's owner's edge list More...

void	set_pos_in_node_edgevector (int callers_index, int position)
	edge keeps index it has in node_ind's edge vector More...

bool	same_edge (int node1, int node2) const
	returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important More...

Real	edge_weight () const

bool	marked_for_deletion () const
	Has this edge indicated that it can be deleted? More...

InteractionGraphBase const *	get_owner () const

InteractionGraphBase *	get_owner ()

Static Public Member Functions
static core::PackerEnergy	get_alternate_state_energy (int first_node_state, int second_node_state, ObjexxFCL::FArray2< core::PackerEnergy > &edge_energy_table)
	static method that looks up the two body energy when the node with the smaller index on an edge is considering an alternate state More...

Private Member Functions
DoubleDensePDNode *	get_dpd_node (int index) const

DoubleDensePDInteractionGraph *	get_dpdig_owner () const

	DoubleDensePDEdge ()

	DoubleDensePDEdge (DoubleDensePDEdge const &)

DoubleDensePDEdge &	operator= (DoubleDensePDEdge const &)

Private Attributes
ObjexxFCL::FArray2D < core::PackerEnergy >	two_body_energies_

core::PackerEnergy	curr_state_energy_

bool	energies_updated_since_last_prep_for_simA_

Additional Inherited Members
Protected Member Functions inherited from core::pack::interaction_graph::EdgeBase
void	mark_edge_for_deletion ()
	Mark this edge so that it can be deleted. More...

int	get_node_index (int index) const

int	get_num_states_for_node (int index) const

NodeBase const *	get_node (int index) const

NodeBase *	get_node (int index)

int	get_edges_position_in_nodes_edge_vector (int index) const

int	which_node (int node_index) const
	is a node the first or second node this edge is incident upon? More...

void	edge_weight (Real)
	protected setter of the edge weight. To be called by derived classes after they have completed the conversion from the previous edge weighting to the new edge weighting. More...

Constructor & Destructor Documentation

core::pack::interaction_graph::DoubleDensePDEdge::DoubleDensePDEdge	(	InteractionGraphBase *	owner,
		int	first_node_ind,
		int	second_node_ind
	)

main constructor - no default nor copy constructors provided

Parameters

owner	- [in] - pointer to the graph that created this node
first_node_ind	- [in] - the index of the smaller-indexed node
second_node_ind	- [in] - the index of the larger-indexed node

core::pack::interaction_graph::DoubleDensePDEdge::~DoubleDensePDEdge ( )

overridedefault

destructor. All dynamically allocated memory is managed by the objects contained inside the DoubleDensePDEdge, so there is no work to be (explicitly) done.

core::pack::interaction_graph::DoubleDensePDEdge::DoubleDensePDEdge ( )

private

Referenced by count_static_memory().

core::pack::interaction_graph::DoubleDensePDEdge::DoubleDensePDEdge ( DoubleDensePDEdge const & )

private

Member Function Documentation

void core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_state_change	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	new_energy
	)

updates bookkeeping information when one of the two nodes changes its state

Parameters

node_ind	- [in] - the index of the node that changed its state
node_state	- [in] - the index of the new state it assumed
new_energy	- [out] - the two body energy produced by the new state and the current state on the other node

Referenced by core::pack::interaction_graph::DoubleDensePDNode::assign_state().

void core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_state_zeroed ( int node_ind )

updates bookkeeping information when one of the two nodes enters its "unassigned" state.

Parameters

node_ind - [in] - the index of the node that has just entered its 0 state

References core::pack::interaction_graph::DoubleDensePDNode::acknowledge_neighbors_state_substitution(), curr_state_energy_, get_dpd_node(), core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), and core::pack::interaction_graph::EdgeBase::get_node_index().

void core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_substitution	(	int	substituted_node_index,
		core::PackerEnergy const	curr_state_energy,
		int	nodes_new_state
	)

inline

update bookkeeping information when one of the nodes an edge is incident upon changes state

Parameters

substituted_node_index	- [in] - index of the node that chagned its state
curr_state_energy	- [in] - the two body energy given the new state
nodes_new_state	- [in] - the state the node just transitioned into
nodes_new_state_sparse_info	- [in] - sparse matrix info for the new state

References curr_state_energy_, get_dpd_node(), core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), and core::pack::interaction_graph::EdgeBase::get_node_index().

Referenced by core::pack::interaction_graph::DoubleDensePDNode::commit_considered_substitution().

void core::pack::interaction_graph::DoubleDensePDEdge::add_to_two_body_energies ( ObjexxFCL::FArray2< core::PackerEnergy > const & res_res_energy_array )

overridevirtual

Adds all the energies stored in the oversized_res_res_energy array to the two body energy table for those states whose amion acid types were previoudsly declared to be amino-acid neighbors. The res-res array should have the dimension (node1->get_num_states() x node2->get_num_states());.

Parameters

res_res_energy_array - [in] - an array containing the state pair energies

Implements core::pack::interaction_graph::PrecomputedPairEnergiesEdge.

void core::pack::interaction_graph::DoubleDensePDEdge::add_to_two_body_energy	(	int const	state1,
		int const	state2,
		core::PackerEnergy const	energy
	)

overridevirtual

adds the input energy to the two body energy for state1 on the node with the smaller index and state2 on the node with the larger index.

Implements core::pack::interaction_graph::PrecomputedPairEnergiesEdge.

References protocols::buns::energy.

void core::pack::interaction_graph::DoubleDensePDEdge::clear_two_body_energy	(	int const	state1,
		int const	state2
	)

overridevirtual

Sets the two-body energy for a pair of states. That is, it overwrites whatever two-body energy there was previously for that state pair with a new energy. Ignores non-neighboring state pairs.

Parameters

state1	- [in] - state index for the node with the smaller index
state2	- [in] - state index for the node with the larger index
energy	- [in] - the energy which replaces the old two-body energy

Implements core::pack::interaction_graph::PrecomputedPairEnergiesEdge.

unsigned int core::pack::interaction_graph::DoubleDensePDEdge::count_dynamic_memory ( ) const

overridevirtual

returns the amount of memory dynamically allocated by the edge and recurses on its parent (in this case, the EdgeBase class)

Reimplemented from core::pack::interaction_graph::EdgeBase.

References core::pack::interaction_graph::EdgeBase::count_dynamic_memory(), and two_body_energies_.

unsigned int core::pack::interaction_graph::DoubleDensePDEdge::count_static_memory ( ) const

overridevirtual

returns sizeof DoubleDensePDEdge if this is the most-derived instance of the class

Implements core::pack::interaction_graph::EdgeBase.

References DoubleDensePDEdge().

void core::pack::interaction_graph::DoubleDensePDEdge::declare_energies_final ( )

overridevirtual

If all of the energies for an edge have been added in, then declare the edge energies final. This may mean that the edge deletes itself.

Implements core::pack::interaction_graph::EdgeBase.

References prepare_for_simulated_annealing().

void core::pack::interaction_graph::DoubleDensePDEdge::force_aa_neighbors	(	int	,
		int
	)

inlineoverridevirtual

Implements core::pack::interaction_graph::FixedBBEdge.

void core::pack::interaction_graph::DoubleDensePDEdge::force_all_aa_neighbors ( )

inlineoverridevirtual

Implements core::pack::interaction_graph::FixedBBEdge.

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDEdge::get_alternate_state_energy	(	int	first_node_state,
		int	second_node_state,
		ObjexxFCL::FArray2< core::PackerEnergy > &	edge_energy_table
	)

inlinestatic

static method that looks up the two body energy when the node with the smaller index on an edge is considering an alternate state

Parameters

first_node_alt_state	- [in] - the alternate state for the lower-indexed node
second_node_orig_state	- [in] - the current state for the higher-indexed node
edge_energy_table	- [in] - the proxy FArray pointing at the edge table connecting the two nodes.

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDEdge::get_current_two_body_energy ( )

returns the two body energy corresponding to the current states assigned to the nodes this edge is incident upon.

References curr_state_energy_.

Referenced by core::pack::interaction_graph::DoubleDensePDNode::update_internal_energy_sums().

DoubleDensePDNode* core::pack::interaction_graph::DoubleDensePDEdge::get_dpd_node ( int index ) const

inlineprivate

References core::pack::interaction_graph::EdgeBase::get_node().

Referenced by acknowledge_state_zeroed(), and acknowledge_substitution().

DoubleDensePDInteractionGraph* core::pack::interaction_graph::DoubleDensePDEdge::get_dpdig_owner ( ) const

inlineprivate

References core::pack::interaction_graph::EdgeBase::get_owner().

bool core::pack::interaction_graph::DoubleDensePDEdge::get_sparse_aa_info	(	int	,
		int
	)		const

inlineoverridevirtual

Implements core::pack::interaction_graph::FixedBBEdge.

core::PackerEnergy core::pack::interaction_graph::DoubleDensePDEdge::get_two_body_energy	(	int const	state1,
		int const	state2
	)		const

overridevirtual

returns the two body energy for a pair of states: 0 if those states are not neighbors

Parameters

state1	- [in] - state index for the node with the smaller index
state2	- [in] - state index for the node with the larger index

Implements core::pack::interaction_graph::PrecomputedPairEnergiesEdge.

References two_body_energies_.

Referenced by core::pack::interaction_graph::DoubleDensePDNode::update_internal_vectors().

int core::pack::interaction_graph::DoubleDensePDEdge::get_two_body_table_size ( ) const

Returns a reference to the first element in the dense two-body energy table. Used to create a proxy array on the nodes for cache efficiency.

returns the memory usage of the two body energy table for this edge

References two_body_energies_.

DoubleDensePDEdge& core::pack::interaction_graph::DoubleDensePDEdge::operator= ( DoubleDensePDEdge const & )

private

void core::pack::interaction_graph::DoubleDensePDEdge::prepare_for_simulated_annealing ( )

overridevirtual

looks at all pair energies, and if they are all 0, deletes itself

Implements core::pack::interaction_graph::EdgeBase.

References energies_updated_since_last_prep_for_simA_, core::pack::interaction_graph::EdgeBase::mark_edge_for_deletion(), and two_body_energies_.

Referenced by declare_energies_final().

void core::pack::interaction_graph::DoubleDensePDEdge::set_edge_weight ( Real weight )

overridevirtual

DANGER: If for some reason one were to reweight edges during simulated annealing then some of the cached energies in the adjacent nodes would be out-of-date; data integrity would be violated an all hell would break loose. The same thing is true if one were to change the energies on any edge during simulated annealing. One simple solution: call blanket_assign_state0 to wipe all cahced energies stored on nodes and then assign_network_state to the state just before the reweighting. Of course, since the annealer itself is tracking the "best" network state, you'd have to worry about its data integrity as well. General advice: don't change energies during simA.

Implements core::pack::interaction_graph::EdgeBase.

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::edge_weight(), and two_body_energies_.

void core::pack::interaction_graph::DoubleDensePDEdge::set_sparse_aa_info ( ObjexxFCL::FArray2_bool const & )

inlineoverridevirtual

Implements core::pack::interaction_graph::FixedBBEdge.

void core::pack::interaction_graph::DoubleDensePDEdge::set_two_body_energy	(	int const	state1,
		int const	state2,
		core::PackerEnergy const	energy
	)

overridevirtual

Sets the two-body energy for a pair of states. That is, it overwrites whatever two-body energy there was previously for that state pair with a new energy. Ignores non-neighboring state pairs.

Parameters

state1	- [in] - state index for the node with the smaller index
state2	- [in] - state index for the node with the larger index
energy	- [in] - the energy which replaces the old two-body energy

Implements core::pack::interaction_graph::PrecomputedPairEnergiesEdge.

References protocols::buns::energy.