#include <SymmLinMemInteractionGraph.hh>

Public Member Functions
	SymmLinearMemEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)

virtual	~SymmLinearMemEdge ()

virtual core::PackerEnergy	get_two_body_energy (int const node1state, int const node2state) const

virtual void	prepare_for_simulated_annealing ()

core::PackerEnergy	get_current_two_body_energy () const

void	acknowledge_state_change (int node_ind, int new_state, int bumped_recent_history_index, int new_state_recent_history_index, core::PackerEnergy &new_energy)

void	acknowledge_state_zeroed (int node_ind)

void	acknowledge_partial_state_change (int node_ind, int new_state, int bumped_recent_history_index, int new_state_recent_history_index)

core::PackerEnergy	get_energy_following_partial_state_assignment ()

void	reset_state_energies (int node_index, int state, int recent_history_id)

core::PackerEnergy	get_energy_for_alt_state (bool store_rpes, int changing_node_index, int alternate_state, int alternate_state_recent_history_index, int other_node_curr_state, int other_node_state_recent_history_index)

void	acknowledge_substitution (int substituted_node_index, core::PackerEnergy const curr_state_energy, int nodes_new_state, int bumped_recent_history_index, int new_state_recent_history_index, int neighbors_curr_state)

int	get_two_body_table_size () const

virtual void	declare_energies_final ()

void	print_current_energy () const

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

virtual void	set_edge_weight (Real weight)

SymmLinearMemNode const *	get_symmlinmem_node (int index) const

SymmLinearMemNode *	get_symmlinmem_node (int index)

SymmLinearMemoryInteractionGraph const *	get_symmlinmem_ig_owner () const

SymmLinearMemoryInteractionGraph *	get_symmlinmem_ig_owner ()

Public Member Functions inherited from core::pack::interaction_graph::SymmOnTheFlyEdge
virtual	~SymmOnTheFlyEdge ()

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

void	add_ProCorrection_values (int node_not_necessarily_proline, int state, core::PackerEnergy bb_nonprobb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_nonprobb_E, core::PackerEnergy sc_probb_E)

core::PackerEnergy	get_proline_correction_for_node (int node_ind, int state) const

bool	long_range_interactions_exist () const

bool	short_range_interactions_exist () const

void	note_long_range_interactions_exist ()

void	note_short_range_interactions_exist ()

ResiduePairEvalType	eval_type (int node_index) const

void	set_residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit)

unsigned char	residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit, int whichnode_restypegroup, int othernode_restypegroup) const

virtual void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &)
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

virtual bool	get_sparse_aa_info (int, int) const
	fullfilling base class virtual member request – however, this function does not quite make sense for a symmetric otf ig, so this is just stubbed out to return true. More...

virtual void	force_aa_neighbors (int, int)
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

virtual void	force_all_aa_neighbors ()
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

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

	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

InteractionGraphBase const *	get_owner () const

InteractionGraphBase *	get_owner ()

Static Public Attributes
static core::PackerEnergy const	NOT_YET_COMPUTED_ENERGY = -1234

Private Member Functions
void	handle_bumped_recent_history_state_for_node (int node_substituted, int node_not_substituted, int bumped_recent_history_index)

void	store_curr_state_energy ()

void	wipe (int node)

	SymmLinearMemEdge ()

	SymmLinearMemEdge (SymmLinearMemEdge const &)

SymmLinearMemEdge &	operator= (SymmLinearMemEdge const &)

Private Attributes
bool	store_rpes_ [2]

ObjexxFCL::FArray2D < core::PackerEnergy >	stored_rpes_ [2]

core::PackerEnergy	curr_state_energy_

core::PackerEnergy	alt_state_energy_

bool	partial_state_assignment_

bool	preped_for_sim_annealing_

Additional Inherited Members
Protected Member Functions inherited from core::pack::interaction_graph::SymmOnTheFlyEdge
core::PackerEnergy	get_proline_correction (int which_node, int state) const

SymmOnTheFlyNode const *	get_otf_node (int which_node) const

SymmOnTheFlyNode *	get_otf_node (int which_node)

SymmOnTheFlyInteractionGraph const *	get_otf_owner () const

SymmOnTheFlyInteractionGraph *	get_otf_owner ()

Protected Member Functions inherited from core::pack::interaction_graph::EdgeBase
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::SymmLinearMemEdge::SymmLinearMemEdge	(	InteractionGraphBase *	owner,
		int	first_node_ind,
		int	second_node_ind
	)

References store_rpes_.

core::pack::interaction_graph::SymmLinearMemEdge::~SymmLinearMemEdge ( )

virtual

core::pack::interaction_graph::SymmLinearMemEdge::SymmLinearMemEdge ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

void core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_partial_state_change	(	int	node_ind,
		int	new_state,
		int	bumped_recent_history_index,
		int	new_state_recent_history_index
	)

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), get_symmlinmem_node(), handle_bumped_recent_history_state_for_node(), and partial_state_assignment_.

Referenced by core::pack::interaction_graph::SymmLinearMemNode::partial_assign_state().

void core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_state_change	(	int	node_ind,
		int	new_state,
		int	bumped_recent_history_index,
		int	new_state_recent_history_index,
		core::PackerEnergy &	new_energy
	)

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), get_symmlinmem_node(), handle_bumped_recent_history_state_for_node(), and store_curr_state_energy().

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

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

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

void core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_substitution	(	int	substituted_node_index,
		core::PackerEnergy const	curr_state_energy,
		int	nodes_new_state,
		int	bumped_recent_history_index,
		int	new_state_recent_history_index,
		int	neighbors_curr_state
	)

inline

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), get_symmlinmem_node(), handle_bumped_recent_history_state_for_node(), and stored_rpes_.

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

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

virtual

Reimplemented from core::pack::interaction_graph::SymmOnTheFlyEdge.

References core::pack::interaction_graph::SymmOnTheFlyEdge::count_dynamic_memory(), and stored_rpes_.

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

virtual

Implements core::pack::interaction_graph::SymmOnTheFlyEdge.

References SymmLinearMemEdge().

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

virtual

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

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::get_current_two_body_energy ( ) const

References curr_state_energy_.

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

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::get_energy_following_partial_state_assignment ( )

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), get_symmlinmem_node(), partial_state_assignment_, and store_curr_state_energy().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::get_energy_for_alt_state	(	bool	store_rpes,
		int	changing_node_index,
		int	alternate_state,
		int	alternate_state_recent_history_index,
		int	other_node_curr_state,
		int	other_node_state_recent_history_index
	)

References core::pack::interaction_graph::debug, and core::pack::interaction_graph::T.

SymmLinearMemoryInteractionGraph const * core::pack::interaction_graph::SymmLinearMemEdge::get_symmlinmem_ig_owner ( ) const

inline

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

SymmLinearMemoryInteractionGraph * core::pack::interaction_graph::SymmLinearMemEdge::get_symmlinmem_ig_owner ( )

inline

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

SymmLinearMemNode const * core::pack::interaction_graph::SymmLinearMemEdge::get_symmlinmem_node ( int index ) const

inline

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

Referenced by acknowledge_partial_state_change(), acknowledge_state_change(), acknowledge_state_zeroed(), acknowledge_substitution(), get_energy_following_partial_state_assignment(), prepare_for_simulated_annealing(), and store_curr_state_energy().

SymmLinearMemNode * core::pack::interaction_graph::SymmLinearMemEdge::get_symmlinmem_node ( int index )

inline

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

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::get_two_body_energy	(	int const	node1state,
		int const	node2state
	)		const

virtual

Implements core::pack::interaction_graph::SymmOnTheFlyEdge.

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

References core::io::serialization::size(), and stored_rpes_.

void core::pack::interaction_graph::SymmLinearMemEdge::handle_bumped_recent_history_state_for_node	(	int	node_substituted,
		int	node_not_substituted,
		int	bumped_recent_history_index
	)

private

Referenced by acknowledge_partial_state_change(), acknowledge_state_change(), and acknowledge_substitution().

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

private

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

virtual

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

References core::pack::interaction_graph::EdgeBase::get_num_states_for_node(), get_symmlinmem_node(), NOT_YET_COMPUTED_ENERGY, preped_for_sim_annealing_, store_rpes_, stored_rpes_, and wipe().

void core::pack::interaction_graph::SymmLinearMemEdge::print_current_energy ( ) const

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

void core::pack::interaction_graph::SymmLinearMemEdge::reset_state_energies	(	int	node_index,
		int	state,
		int	recent_history_id
	)

References core::pack::interaction_graph::EdgeBase::get_node_index(), core::pack::interaction_graph::EdgeBase::get_num_states_for_node(), NOT_YET_COMPUTED_ENERGY, and stored_rpes_.

Referenced by core::pack::interaction_graph::SymmLinearMemNode::prepare_for_simulated_annealing().

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

virtual

DANGER: this will not update the cached energies on the nodes this edge is incident upon.

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

References core::pack::interaction_graph::EdgeBase::edge_weight(), NOT_YET_COMPUTED_ENERGY, and stored_rpes_.

void core::pack::interaction_graph::SymmLinearMemEdge::store_curr_state_energy ( )

private

References curr_state_energy_, core::pack::interaction_graph::SymmLinearMemNode::get_curr_state_recent_state_id(), core::pack::interaction_graph::SymmLinearMemNode::get_current_state(), get_symmlinmem_node(), store_rpes_, and stored_rpes_.

Referenced by acknowledge_state_change(), and get_energy_following_partial_state_assignment().

void core::pack::interaction_graph::SymmLinearMemEdge::wipe ( int node )

private

References NOT_YET_COMPUTED_ENERGY, and stored_rpes_.

Referenced by prepare_for_simulated_annealing().

Member Data Documentation

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::alt_state_energy_

private

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::curr_state_energy_

private

Referenced by acknowledge_partial_state_change(), acknowledge_state_change(), acknowledge_state_zeroed(), acknowledge_substitution(), get_current_two_body_energy(), get_energy_following_partial_state_assignment(), print_current_energy(), and store_curr_state_energy().

core::PackerEnergy const core::pack::interaction_graph::SymmLinearMemEdge::NOT_YET_COMPUTED_ENERGY = -1234

static

Referenced by prepare_for_simulated_annealing(), reset_state_energies(), set_edge_weight(), and wipe().

bool core::pack::interaction_graph::SymmLinearMemEdge::partial_state_assignment_

private

Referenced by acknowledge_partial_state_change(), and get_energy_following_partial_state_assignment().

bool core::pack::interaction_graph::SymmLinearMemEdge::preped_for_sim_annealing_

private

Referenced by prepare_for_simulated_annealing().

bool core::pack::interaction_graph::SymmLinearMemEdge::store_rpes_[2]

private

Referenced by prepare_for_simulated_annealing(), store_curr_state_energy(), and SymmLinearMemEdge().

ObjexxFCL::FArray2D< core::PackerEnergy > core::pack::interaction_graph::SymmLinearMemEdge::stored_rpes_[2]

private

Referenced by acknowledge_substitution(), count_dynamic_memory(), get_two_body_table_size(), prepare_for_simulated_annealing(), reset_state_energies(), set_edge_weight(), store_curr_state_energy(), and wipe().

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

src/core/pack/interaction_graph/SymmLinMemInteractionGraph.hh
src/core/pack/interaction_graph/SymmLinMemInteractionGraph.cc

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation