#include <LinearMemoryInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::LinearMemEdge:

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

	~LinearMemEdge () override

void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &) override

void	force_aa_neighbors (int node1aa, int node2aa) override

void	force_all_aa_neighbors () override

bool	get_sparse_aa_info (int node1aa, int node2aa) const override

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

void	prepare_for_simulated_annealing () override

core::PackerEnergy	get_current_two_body_energy () const

void	acknowledge_state_change (int node_ind, int new_state, SparseMatrixIndex const &new_state_sparse_info, 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, SparseMatrixIndex const &new_state_sparse_info, 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, SparseMatrixIndex const &nodes_new_state_sparse_info, int bumped_recent_history_index, int new_state_recent_history_index, int neighbors_curr_state)

int	get_two_body_table_size () const

void	declare_energies_final () override

void	print_current_energy () const

ObjexxFCL::FArray2D< unsigned char > const &	get_sparse_aa_neighbor_info ()

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override

void	set_edge_weight (Real weight) override

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

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

void	set_ProCorrection_values (int node_not_necessarily_proline, int state, core::PackerEnergy bb_regbb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_regbb_E, core::PackerEnergy sc_probb_E)

void	set_GlyCorrection_values (int node_not_necessarily_glycine, int state, core::PackerEnergy bb_regbb_E, core::PackerEnergy bb_glybb_E, core::PackerEnergy sc_regbb_E, core::PackerEnergy sc_glybb_E)

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

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

unsigned int	count_dynamic_memory () const override

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

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 Attributes
static core::PackerEnergy const	NOT_YET_COMPUTED_ENERGY = -1234

Protected Member Functions
void	declare_energies_final_no_deletion ()

void	prepare_for_simulated_annealing_no_deletion ()

bool	pd_edge_table_all_zeros () const

Protected Member Functions inherited from core::pack::interaction_graph::OnTheFlyEdge
core::PackerEnergy	get_proline_correction (int which_node, int state) const

core::PackerEnergy	get_glycine_correction (int which_node, int state) const

OnTheFlyNode const *	get_otf_node (int which_node) const

OnTheFlyNode *	get_otf_node (int which_node)

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...

Private Member Functions
LinearMemNode const *	get_linmem_node (int index) const

LinearMemNode *	get_linmem_node (int index)

LinearMemoryInteractionGraph const *	get_linmem_ig_owner () const

LinearMemoryInteractionGraph *	get_linmem_ig_owner ()

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)

	LinearMemEdge ()

	LinearMemEdge (LinearMemEdge const &)

LinearMemEdge &	operator= (LinearMemEdge const &)

Private Attributes
bool	store_rpes_ [2]

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

ObjexxFCL::FArray2D< unsigned char >	sparse_aa_neighbors_

core::PackerEnergy	curr_state_energy_

core::PackerEnergy	alt_state_energy_

bool	partial_state_assignment_

bool	preped_for_sim_annealing_

Constructor & Destructor Documentation

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

References store_rpes_.

core::pack::interaction_graph::LinearMemEdge::~LinearMemEdge ( )

overridedefault

core::pack::interaction_graph::LinearMemEdge::LinearMemEdge ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

void core::pack::interaction_graph::LinearMemEdge::acknowledge_partial_state_change	(	int	node_ind,
		int	new_state,
		SparseMatrixIndex const &	new_state_sparse_info,
		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(), get_linmem_node(), core::pack::interaction_graph::EdgeBase::get_node_index(), handle_bumped_recent_history_state_for_node(), and partial_state_assignment_.

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

void core::pack::interaction_graph::LinearMemEdge::acknowledge_state_change	(	int	node_ind,
		int	new_state,
		SparseMatrixIndex const &	new_state_sparse_info,
		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(), get_linmem_node(), core::pack::interaction_graph::EdgeBase::get_node_index(), handle_bumped_recent_history_state_for_node(), and store_curr_state_energy().

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

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

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), get_linmem_node(), core::pack::interaction_graph::EdgeBase::get_node_index(), core::pack::interaction_graph::SparseMatrixIndex::set_aa_type(), and core::pack::interaction_graph::SparseMatrixIndex::set_state_ind_for_this_aa_type().

void core::pack::interaction_graph::LinearMemEdge::acknowledge_substitution	(	int	substituted_node_index,
		core::PackerEnergy const	curr_state_energy,
		int	nodes_new_state,
		SparseMatrixIndex const &	nodes_new_state_sparse_info,
		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(), get_linmem_node(), core::pack::interaction_graph::EdgeBase::get_node_index(), handle_bumped_recent_history_state_for_node(), and stored_rpes_.

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

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

overridevirtual

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

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

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

overridevirtual

Implements core::pack::interaction_graph::OnTheFlyEdge.

References LinearMemEdge().

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

overridevirtual

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

void core::pack::interaction_graph::LinearMemEdge::declare_energies_final_no_deletion ( )

inlineprotected

References prepare_for_simulated_annealing().

void core::pack::interaction_graph::LinearMemEdge::force_aa_neighbors	(	int	node1aa,
		int	node2aa
	)

overridevirtual

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

References sparse_aa_neighbors_.

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

overridevirtual

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

References get_linmem_ig_owner(), core::pack::interaction_graph::OnTheFlyInteractionGraph::get_num_aatypes(), and sparse_aa_neighbors_.

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

References curr_state_energy_.

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

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

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

core::PackerEnergy core::pack::interaction_graph::LinearMemEdge::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().

LinearMemoryInteractionGraph const * core::pack::interaction_graph::LinearMemEdge::get_linmem_ig_owner ( ) const

inlineprivate

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

Referenced by force_all_aa_neighbors(), and set_sparse_aa_info().

LinearMemoryInteractionGraph * core::pack::interaction_graph::LinearMemEdge::get_linmem_ig_owner ( )

inlineprivate

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

LinearMemNode const * core::pack::interaction_graph::LinearMemEdge::get_linmem_node ( int index ) const

inlineprivate

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().

LinearMemNode * core::pack::interaction_graph::LinearMemEdge::get_linmem_node ( int index )

inlineprivate

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

bool core::pack::interaction_graph::LinearMemEdge::get_sparse_aa_info	(	int	node1aa,
		int	node2aa
	)		const

overridevirtual

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

References sparse_aa_neighbors_.

ObjexxFCL::FArray2D< unsigned char > const & core::pack::interaction_graph::LinearMemEdge::get_sparse_aa_neighbor_info ( )

References sparse_aa_neighbors_.

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

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

overridevirtual

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

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

References stored_rpes_.

void core::pack::interaction_graph::LinearMemEdge::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().

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

private

bool core::pack::interaction_graph::LinearMemEdge::pd_edge_table_all_zeros ( ) const

inlineprotected

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

overridevirtual

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

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

Referenced by declare_energies_final_no_deletion(), and prepare_for_simulated_annealing_no_deletion().

void core::pack::interaction_graph::LinearMemEdge::prepare_for_simulated_annealing_no_deletion ( )

inlineprotected

References prepare_for_simulated_annealing().

void core::pack::interaction_graph::LinearMemEdge::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::LinearMemEdge::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::LinearMemNode::prepare_for_simulated_annealing().

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

overridevirtual

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::LinearMemEdge::set_sparse_aa_info ( ObjexxFCL::FArray2_bool const & aa_neighbors )

overridevirtual

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

References get_linmem_ig_owner(), core::pack::interaction_graph::OnTheFlyInteractionGraph::get_num_aatypes(), and sparse_aa_neighbors_.

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

private

References curr_state_energy_, core::pack::interaction_graph::LinearMemNode::get_curr_state_recent_state_id(), core::pack::interaction_graph::LinearMemNode::get_current_state(), get_linmem_node(), store_rpes_, and stored_rpes_.

Referenced by acknowledge_state_change(), and get_energy_following_partial_state_assignment().

void core::pack::interaction_graph::LinearMemEdge::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::LinearMemEdge::alt_state_energy_

private

core::PackerEnergy core::pack::interaction_graph::LinearMemEdge::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::LinearMemEdge::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::LinearMemEdge::partial_state_assignment_

private

Referenced by acknowledge_partial_state_change(), and get_energy_following_partial_state_assignment().

bool core::pack::interaction_graph::LinearMemEdge::preped_for_sim_annealing_

private

Referenced by prepare_for_simulated_annealing().

ObjexxFCL::FArray2D< unsigned char > core::pack::interaction_graph::LinearMemEdge::sparse_aa_neighbors_

private

Referenced by count_dynamic_memory(), force_aa_neighbors(), force_all_aa_neighbors(), get_sparse_aa_info(), get_sparse_aa_neighbor_info(), and set_sparse_aa_info().

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

private

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

ObjexxFCL::FArray2D< core::PackerEnergy > core::pack::interaction_graph::LinearMemEdge::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/LinearMemoryInteractionGraph.hh
src/core/pack/interaction_graph/LinearMemoryInteractionGraph.cc

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation