#include <DoubleLazyInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::DoubleLazyEdge:

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

	~DoubleLazyEdge () 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
	returns whether two amino acid types are represented as neighbors More...

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

core::PackerEnergy	get_two_body_energy_smi (int const node1state, int const node2state, SparseMatrixIndex const &node1info, SparseMatrixIndex const &node2info) const

void	declare_energies_final () 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, 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)

core::PackerEnergy	get_energy_following_partial_state_assignment ()

void	acknowledge_substitution (int substituted_node_index, core::PackerEnergy const curr_state_energy, int nodes_new_state, SparseMatrixIndex const &nodes_new_state_sparse_info)

void	set_edge_weight (Real weight) override

int	get_two_body_table_size () const

void	print_current_energy () const

bool	build_sc_only_rotamer ()

ObjexxFCL::FArray2D < core::PackerEnergy >	get_aa_submatrix_energies (int node1aa, int node2aa) const

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override

unsigned int	actual_twobody_memory_use () const

unsigned int	potential_twobody_memory_use () const

void	set_edge_index (int index)
	For use by the DoubleLazyInteractionGraph only; sets the edge index for this edge – this is an arbitrary index, but is used to so that the DLIG can communicate back and forth with this edge. More...

int	drop_aa_submatrix (int submat_ind) const
	For use by the DoubleLazyInteractionGraph only; if the DLIG is in "memory conservation" mode, then it may request that its edges drop certain amino acid submatrices which have not been activated for a "long time." This function will cause an amino-acid submatrix to be dropped, and will return the number of bytes that have been freed in the process. "const" but accesses mutable data. More...

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
void	prep_aa_submatrix (int node1aa, int node2aa) const

core::PackerEnergy	read_aa_submatrix (SparseMatrixIndex node1info, SparseMatrixIndex node2info) const

void	set_aa_submatrix (SparseMatrixIndex node1info, SparseMatrixIndex node2info, core::PackerEnergy setting) const

void	get_energy_for_state_pair (int nodes_states[2], SparseMatrixIndex sparse_matrix_indices[2])

DoubleLazyNode const *	get_dlazy_node (int index) const

DoubleLazyNode *	get_dlazy_node (int index)

DoubleLazyInteractionGraph const *	get_dlazy_ig_owner () const

DoubleLazyInteractionGraph *	get_dlazy_ig_owner ()

void	wipe_two_body_energies_for_node_state (int node, int state)

int	submatrix_index (int nod1aa, int node2aa) const

int	submatrix_size (int node1aa, int node2aa) const

std::pair< int, int >	aa_indices_from_submatrix_index (int submat_ind) const

	DoubleLazyEdge ()

	DoubleLazyEdge (DoubleLazyEdge const &)

DoubleLazyEdge &	operator= (DoubleLazyEdge const &)

Private Attributes
ObjexxFCL::FArray2D< unsigned char >	sparse_aa_neighbors_
	record which amino acid pairs are neighbors More...

ObjexxFCL::FArray2D < ObjexxFCL::FArray2D < core::PackerEnergy > * >	two_body_energies_

core::PackerEnergy	curr_state_energy_

bool	partial_state_assignment_

bool	ran_annealing_since_pair_energy_table_cleared_

int	edge_index_

Constructor & Destructor Documentation

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

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

core::pack::interaction_graph::DoubleLazyEdge::~DoubleLazyEdge ( )

override

explicity deallocate the FArrays that were dynamically allocated

References two_body_energies_.

core::pack::interaction_graph::DoubleLazyEdge::DoubleLazyEdge ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

std::pair< int, int > core::pack::interaction_graph::DoubleLazyEdge::aa_indices_from_submatrix_index ( int submat_ind ) const

private

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

Referenced by drop_aa_submatrix().

void core::pack::interaction_graph::DoubleLazyEdge::acknowledge_partial_state_change	(	int	node_ind,
		int	new_state,
		SparseMatrixIndex const &	new_state_sparse_info
	)

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References core::pack::interaction_graph::DoubleLazyNode::acknowledge_neighbors_partial_state_substitution(), curr_state_energy_, get_dlazy_node(), core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), and partial_state_assignment_.

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

void core::pack::interaction_graph::DoubleLazyEdge::acknowledge_state_change	(	int	node_ind,
		int	new_state,
		SparseMatrixIndex const &	new_state_sparse_info,
		core::PackerEnergy &	new_energy
	)

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References core::pack::interaction_graph::DoubleLazyNode::acknowledge_neighbors_state_substitution(), curr_state_energy_, core::pack::interaction_graph::DoubleLazyNode::get_current_state(), get_dlazy_node(), core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), get_energy_for_state_pair(), and core::pack::interaction_graph::EdgeBase::get_node_index().

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

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

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References core::pack::interaction_graph::DoubleLazyNode::acknowledge_neighbors_state_substitution(), curr_state_energy_, get_dlazy_node(), core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), 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().

Referenced by core::pack::interaction_graph::DoubleLazyNode::assign_zero_state().

void core::pack::interaction_graph::DoubleLazyEdge::acknowledge_substitution	(	int	substituted_node_index,
		core::PackerEnergy const	curr_state_energy,
		int	nodes_new_state,
		SparseMatrixIndex const &	nodes_new_state_sparse_info
	)

inline

References core::pack::interaction_graph::DoubleLazyNode::acknowledge_neighbors_state_substitution(), curr_state_energy_, get_dlazy_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::DoubleLazyNode::commit_considered_substitution().

unsigned int core::pack::interaction_graph::DoubleLazyEdge::actual_twobody_memory_use ( ) const

References two_body_energies_.

Referenced by count_dynamic_memory(), and core::pack::interaction_graph::DoubleLazyInteractionGraph::~DoubleLazyInteractionGraph().

bool core::pack::interaction_graph::DoubleLazyEdge::build_sc_only_rotamer ( )

inline

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

overridevirtual

add up all the submatrices

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

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

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

overridevirtual

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

References DoubleLazyEdge().

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

overridevirtual

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

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

inlineprotected

References prepare_for_simulated_annealing().

int core::pack::interaction_graph::DoubleLazyEdge::drop_aa_submatrix ( int submat_ind ) const

For use by the DoubleLazyInteractionGraph only; if the DLIG is in "memory conservation" mode, then it may request that its edges drop certain amino acid submatrices which have not been activated for a "long time." This function will cause an amino-acid submatrix to be dropped, and will return the number of bytes that have been freed in the process. "const" but accesses mutable data.

References aa_indices_from_submatrix_index(), submatrix_size(), and two_body_energies_.

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

overridevirtual

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

References sparse_aa_neighbors_.

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

overridevirtual

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

References ran_annealing_since_pair_energy_table_cleared_, and sparse_aa_neighbors_.

ObjexxFCL::FArray2D< core::PackerEnergy > core::pack::interaction_graph::DoubleLazyEdge::get_aa_submatrix_energies	(	int	node1aa,
		int	node2aa
	)		const

References core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), edge_index_, get_dlazy_ig_owner(), get_dlazy_node(), core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::OnTheFlyEdge::get_otf_node(), core::pack::interaction_graph::OnTheFlyNode::get_state_offset_for_aatype(), NOT_YET_COMPUTED_ENERGY, core::pack::interaction_graph::DoubleLazyInteractionGraph::note_submatrix_accessed(), prep_aa_submatrix(), sparse_aa_neighbors_, submatrix_index(), and two_body_energies_.

Referenced by core::pack::interaction_graph::DoubleLazyInteractionGraph::get_aa_submatrix_energies_for_edge().

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

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References curr_state_energy_.

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

DoubleLazyInteractionGraph const * core::pack::interaction_graph::DoubleLazyEdge::get_dlazy_ig_owner ( ) const

inlineprivate

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

Referenced by aa_indices_from_submatrix_index(), get_aa_submatrix_energies(), prep_aa_submatrix(), and submatrix_index().

DoubleLazyInteractionGraph * core::pack::interaction_graph::DoubleLazyEdge::get_dlazy_ig_owner ( )

inlineprivate

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

DoubleLazyNode const * core::pack::interaction_graph::DoubleLazyEdge::get_dlazy_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_aa_submatrix_energies(), get_energy_following_partial_state_assignment(), potential_twobody_memory_use(), prep_aa_submatrix(), and submatrix_size().

DoubleLazyNode * core::pack::interaction_graph::DoubleLazyEdge::get_dlazy_node ( int index )

inlineprivate

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

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

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References curr_state_energy_, core::pack::interaction_graph::DoubleLazyNode::get_current_state(), get_dlazy_node(), get_energy_for_state_pair(), core::pack::interaction_graph::DoubleLazyNode::get_sparse_mat_info_for_curr_state(), and partial_state_assignment_.

void core::pack::interaction_graph::DoubleLazyEdge::get_energy_for_state_pair	(	int	nodes_states[2],
		SparseMatrixIndex	sparse_matrix_indices[2]
	)

private

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References curr_state_energy_, get_two_body_energy_smi(), and sparse_aa_neighbors_.

Referenced by acknowledge_state_change(), and get_energy_following_partial_state_assignment().

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

overridevirtual

returns whether two amino acid types are represented as neighbors

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

References sparse_aa_neighbors_.

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

overridevirtual

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

References core::pack::interaction_graph::OnTheFlyEdge::get_otf_node(), core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state(), and get_two_body_energy_smi().

core::PackerEnergy core::pack::interaction_graph::DoubleLazyEdge::get_two_body_energy_smi	(	int const	node1state,
		int const	node2state,
		SparseMatrixIndex const &	node1info,
		SparseMatrixIndex const &	node2info
	)		const

References core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::EdgeBase::edge_weight(), core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::OnTheFlyEdge::get_otf_node(), NOT_YET_COMPUTED_ENERGY, prep_aa_submatrix(), read_aa_submatrix(), set_aa_submatrix(), and sparse_aa_neighbors_.

Referenced by get_energy_for_state_pair(), and get_two_body_energy().

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

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

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

private

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

inlineprotected

unsigned int core::pack::interaction_graph::DoubleLazyEdge::potential_twobody_memory_use ( ) const

References get_dlazy_node(), core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_types(), sparse_aa_neighbors_, and two_body_energies_.

Referenced by core::pack::interaction_graph::DoubleLazyInteractionGraph::~DoubleLazyInteractionGraph().

void core::pack::interaction_graph::DoubleLazyEdge::prep_aa_submatrix	(	int	node1aa,
		int	node2aa
	)		const

private

– const to be called within const functions; updates mutable data

References edge_index_, get_dlazy_ig_owner(), get_dlazy_node(), core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_types(), NOT_YET_COMPUTED_ENERGY, core::pack::interaction_graph::DoubleLazyInteractionGraph::note_submatrix_added(), sparse_aa_neighbors_, submatrix_index(), submatrix_size(), and two_body_energies_.

Referenced by get_aa_submatrix_energies(), and get_two_body_energy_smi().

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

overridevirtual

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

References core::pack::interaction_graph::EdgeBase::mark_edge_for_deletion(), ran_annealing_since_pair_energy_table_cleared_, and sparse_aa_neighbors_.

Referenced by declare_energies_final_no_deletion(), and prepare_for_simulated_annealing_no_deletion().

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

inlineprotected

References prepare_for_simulated_annealing().

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

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

core::PackerEnergy core::pack::interaction_graph::DoubleLazyEdge::read_aa_submatrix	(	SparseMatrixIndex	node1info,
		SparseMatrixIndex	node2info
	)		const

private

References core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), core::pack::interaction_graph::SparseMatrixIndex::get_state_ind_for_this_aa_type(), and two_body_energies_.

Referenced by get_two_body_energy_smi().

void core::pack::interaction_graph::DoubleLazyEdge::set_aa_submatrix	(	SparseMatrixIndex	node1info,
		SparseMatrixIndex	node2info,
		core::PackerEnergy	setting
	)		const

private

updates mutable data

References core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), core::pack::interaction_graph::SparseMatrixIndex::get_state_ind_for_this_aa_type(), and two_body_energies_.

Referenced by get_two_body_energy_smi().

void core::pack::interaction_graph::DoubleLazyEdge::set_edge_index ( int index )

For use by the DoubleLazyInteractionGraph only; sets the edge index for this edge – this is an arbitrary index, but is used to so that the DLIG can communicate back and forth with this edge.

This function is only invoked if the graph is going to attempt to use a memory-use cap. The edge_index_ serves to both identify that the memory-use cap is in effect, and to allow efficient communication between the graph and its edges.

References edge_index_.

Referenced by core::pack::interaction_graph::DoubleLazyInteractionGraph::prepare_graph_for_simulated_annealing().

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

overridevirtual

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

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

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

overridevirtual

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

References NOT_YET_COMPUTED_ENERGY, ran_annealing_since_pair_energy_table_cleared_, sparse_aa_neighbors_, and two_body_energies_.

int core::pack::interaction_graph::DoubleLazyEdge::submatrix_index	(	int	node1aa,
		int	node2aa
	)		const

private

– node1aa and node2aa are both indexed from 1

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

Referenced by get_aa_submatrix_energies(), and prep_aa_submatrix().

int core::pack::interaction_graph::DoubleLazyEdge::submatrix_size	(	int	node1aa,
		int	node2aa
	)		const

private

References get_dlazy_node(), and core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_types().

Referenced by drop_aa_submatrix(), and prep_aa_submatrix().

void core::pack::interaction_graph::DoubleLazyEdge::wipe_two_body_energies_for_node_state	(	int	node,
		int	state
	)

private

Member Data Documentation

core::PackerEnergy core::pack::interaction_graph::DoubleLazyEdge::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(), get_energy_for_state_pair(), and print_current_energy().

int core::pack::interaction_graph::DoubleLazyEdge::edge_index_

private

Referenced by get_aa_submatrix_energies(), prep_aa_submatrix(), and set_edge_index().

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

static

Referenced by get_aa_submatrix_energies(), get_two_body_energy_smi(), prep_aa_submatrix(), set_edge_weight(), and set_sparse_aa_info().

bool core::pack::interaction_graph::DoubleLazyEdge::partial_state_assignment_

private

Referenced by acknowledge_partial_state_change(), and get_energy_following_partial_state_assignment().

bool core::pack::interaction_graph::DoubleLazyEdge::ran_annealing_since_pair_energy_table_cleared_

private

Referenced by force_all_aa_neighbors(), prepare_for_simulated_annealing(), and set_sparse_aa_info().

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

private

record which amino acid pairs are neighbors

Referenced by count_dynamic_memory(), force_aa_neighbors(), force_all_aa_neighbors(), get_aa_submatrix_energies(), get_energy_for_state_pair(), get_sparse_aa_info(), get_two_body_energy_smi(), potential_twobody_memory_use(), prep_aa_submatrix(), prepare_for_simulated_annealing(), and set_sparse_aa_info().

ObjexxFCL::FArray2D< ObjexxFCL::FArray2D< core::PackerEnergy > * > core::pack::interaction_graph::DoubleLazyEdge::two_body_energies_

mutableprivate

Allocate the amino-acid submatrices of the two-body energy table only as needed. In a more advanced version of this graph, these submatrices would be deleted again (and possibly re-instantiated!) after a long time had passed since they were last useful.

Referenced by actual_twobody_memory_use(), count_dynamic_memory(), drop_aa_submatrix(), get_aa_submatrix_energies(), potential_twobody_memory_use(), prep_aa_submatrix(), read_aa_submatrix(), set_aa_submatrix(), set_edge_weight(), set_sparse_aa_info(), and ~DoubleLazyEdge().

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

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

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