#include <LazyInteractionGraph.hh>

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

virtual	~LazyEdge ()

virtual void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &)

virtual void	force_aa_neighbors (int node1aa, int node2aa)
	re-allocates two-body energy table after forcing a pair of amino acids to become neighbors that were not initially declared to be neighbors More...

virtual void	force_all_aa_neighbors ()
	re-allocates two-body energy table after forcing a pair of amino acids to become neighbors that were not initially declared to be neighbors More...

virtual bool	get_sparse_aa_info (int node1aa, int node2aa) const
	returns whether two amino acid types are represented as neighbors More...

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

virtual void	declare_energies_final ()

virtual void	prepare_for_simulated_annealing ()

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)

core::PackerEnergy &	get_edge_table_ptr ()

int	get_two_body_table_size () const

void	print_current_energy () const

bool	build_sc_only_rotamer ()

ObjexxFCL::FArray2D_int const &	get_offsets_for_aatypes ()

utility::vector1< int > const &	get_second_node_num_states_per_aa ()

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

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

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

	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_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

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 Member Functions
static core::PackerEnergy	get_alternate_state_energy_first_node (int first_node_alt_state, int second_node_orig_state, SparseMatrixIndex const &second_node_orig_state_sparse_info, int first_node_state_offset_minus_1, int second_node_curr_num_states_per_aatype, int aa_neighbor_offset, ObjexxFCL::FArray1< core::PackerEnergy > &edge_energy_table)

static core::PackerEnergy	get_alternate_state_energy_second_node (int first_node_orig_state, int second_node_alt_state, SparseMatrixIndex const &first_node_orig_state_sparse_info, SparseMatrixIndex const &second_node_alternate_state_sparse_info, int second_node_alt_state_num_states_per_aatype, int aa_neighbor_offset, ObjexxFCL::FArray1< core::PackerEnergy > &edge_energy_table)

static void	store_interaction_energy_first_node (SparseMatrixIndex const &second_node_orig_state_sparse_info, int first_node_state_offset_minus_1, int second_node_curr_num_states_per_aatype, int aa_neighbor_offset, ObjexxFCL::FArray1< core::PackerEnergy > &edge_energy_table, core::PackerEnergy interaction_energy)

static void	store_interaction_energy_second_node (SparseMatrixIndex const &first_node_orig_state_sparse_info, SparseMatrixIndex const &second_node_alternate_state_sparse_info, int second_node_alt_state_num_states_per_aatype, int aa_neighbor_offset, ObjexxFCL::FArray1< core::PackerEnergy > &edge_energy_table, core::PackerEnergy interaction_energy)

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

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

LazyNode const *	get_lazy_node (int index) const

LazyNode *	get_lazy_node (int index)

LazyInteractionGraph const *	get_lazy_ig_owner () const

LazyInteractionGraph *	get_lazy_ig_owner ()

void	wipe_two_body_energies_for_node_state (int node, int state)

	LazyEdge ()

	LazyEdge (LazyEdge const &)

LazyEdge &	operator= (LazyEdge const &)

Private Attributes
AminoAcidNeighborSparseMatrix < core::PackerEnergy >	two_body_energies_

core::PackerEnergy	curr_state_energy_

bool	partial_state_assignment_

bool	ran_annealing_since_pair_energy_table_cleared_

Constructor & Destructor Documentation

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

LazyEdge::LazyEdge

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par Global Read:

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Authors: apl

Last Modified:

core::pack::interaction_graph::LazyEdge::~LazyEdge ( )

virtual

LazyEdge::~LazyEdge()

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par Global Read:

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Authors: apl

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core::pack::interaction_graph::LazyEdge::LazyEdge ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

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

LazyEdge::acknowledge_partial_state_change

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par Global Read:

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Authors: apl

Last Modified:

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

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

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

LazyEdge::acknowledge_state_change

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par Global Read:

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Authors: apl

Last Modified:

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

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

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

LazyEdge::acknowledge_state_zeroed

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par Global Read:

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Authors: apl

Last Modified:

References core::pack::interaction_graph::LazyNode::acknowledge_neighbors_state_substitution(), curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), get_lazy_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().

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

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

inline

LazyEdge::acknowledge_substitution

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par Global Read:

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Authors: apl

Last Modified:

References core::pack::interaction_graph::LazyNode::acknowledge_neighbors_state_substitution(), curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), get_lazy_node(), and core::pack::interaction_graph::EdgeBase::get_node_index().

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

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

inline

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

virtual

Reimplemented from core::pack::interaction_graph::OnTheFlyEdge.

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

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

virtual

LazyEdge::getMemoryUsageInBytes

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Authors: apl

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

References LazyEdge().

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

virtual

LazyEdge::declare_energies_final

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par Global Read:

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Authors: apl

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

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

inlineprotected

References prepare_for_simulated_annealing().

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

virtual

re-allocates two-body energy table after forcing a pair of amino acids to become neighbors that were not initially declared to be neighbors

Parameters

node1aa	- [in] - the amino acid type for the node with the smaller index
node2aa	- [in] - the amino acid type for the node with the larger index

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

References NOT_YET_COMPUTED_ENERGY, ran_annealing_since_pair_energy_table_cleared_, and two_body_energies_.

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

virtual

re-allocates two-body energy table after forcing a pair of amino acids to become neighbors that were not initially declared to be neighbors

Parameters

node1aa	- [in] - the amino acid type for the node with the smaller index
node2aa	- [in] - the amino acid type for the node with the larger index

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

References NOT_YET_COMPUTED_ENERGY, ran_annealing_since_pair_energy_table_cleared_, and two_body_energies_.

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

References core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), get_lazy_node(), core::pack::interaction_graph::OnTheFlyEdge::get_otf_node(), core::pack::interaction_graph::OnTheFlyNode::get_state_offset_for_aatype(), NOT_YET_COMPUTED_ENERGY, and two_body_energies_.

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

core::PackerEnergy core::pack::interaction_graph::LazyEdge::get_alternate_state_energy_first_node	(	int	first_node_alt_state,
		int	second_node_orig_state,
		SparseMatrixIndex const &	second_node_orig_state_sparse_info,
		int	first_node_state_offset_minus_1,
		int	second_node_curr_num_states_per_aatype,
		int	aa_neighbor_offset,
		ObjexxFCL::FArray1< core::PackerEnergy > &	edge_energy_table
	)

inlinestatic

LazyEdge::get_alternate_state_energy_first_node

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Authors: apl

Last Modified:

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get().

core::PackerEnergy core::pack::interaction_graph::LazyEdge::get_alternate_state_energy_second_node	(	int	first_node_orig_state,
		int	second_node_alt_state,
		SparseMatrixIndex const &	first_node_orig_state_sparse_info,
		SparseMatrixIndex const &	second_node_alternate_state_sparse_info,
		int	second_node_alt_state_num_states_per_aatype,
		int	aa_neighbor_offset,
		ObjexxFCL::FArray1< core::PackerEnergy > &	edge_energy_table
	)

inlinestatic

LazyEdge::get_alternate_state_energy_second_node

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par Global Read:

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Authors: apl

Last Modified:

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get().

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

LazyEdge::get_current_two_body_energy

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par Global Read:

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Authors: apl

Last Modified:

References curr_state_energy_.

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

core::PackerEnergy & core::pack::interaction_graph::LazyEdge::get_edge_table_ptr ( )

LazyEdge::get_edge_table_ptr

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par Global Read:

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Authors: apl

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References two_body_energies_.

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

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

LazyEdge::get_energy_following_partial_state_assignment

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par Global Read:

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Authors: apl

Last Modified:

References curr_state_energy_, core::pack::interaction_graph::LazyNode::get_current_state(), get_energy_for_state_pair(), get_lazy_node(), core::pack::interaction_graph::LazyNode::get_sparse_mat_info_for_curr_state(), and partial_state_assignment_.

void core::pack::interaction_graph::LazyEdge::get_energy_for_state_pair	(	int	nodes_states[2],
		SparseMatrixIndex	sparse_matrix_indices_[2]
	)

private

LazyEdge::get_energy_for_state_pair

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par Global Read:

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References:

Authors: apl

Last Modified:

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), get_lazy_node(), NOT_YET_COMPUTED_ENERGY, and two_body_energies_.

Referenced by acknowledge_state_change(), and get_energy_following_partial_state_assignment().

LazyInteractionGraph const * core::pack::interaction_graph::LazyEdge::get_lazy_ig_owner ( ) const

inlineprivate

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

LazyInteractionGraph * core::pack::interaction_graph::LazyEdge::get_lazy_ig_owner ( )

inlineprivate

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

LazyNode const * core::pack::interaction_graph::LazyEdge::get_lazy_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(), get_energy_for_state_pair(), get_second_node_num_states_per_aa(), and wipe_two_body_energies_for_node_state().

LazyNode * core::pack::interaction_graph::LazyEdge::get_lazy_node ( int index )

inlineprivate

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

ObjexxFCL::FArray2D_int const & core::pack::interaction_graph::LazyEdge::get_offsets_for_aatypes ( )

LazyEdge::get_offsets_for_aatypes

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par Global Read:

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Authors: apl

Last Modified:

References two_body_energies_.

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

utility::vector1< int > const & core::pack::interaction_graph::LazyEdge::get_second_node_num_states_per_aa ( )

LazyEdge::get_second_node_num_states_per_aa

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par Global Read:

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Authors: apl

Last Modified:

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

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

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

virtual

returns whether two amino acid types are represented as neighbors

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

References two_body_energies_.

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

virtual

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

References core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), 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_sparse_mat_info_for_state(), NOT_YET_COMPUTED_ENERGY, and two_body_energies_.

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

LazyEdge::get_two_body_table_size

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par Global Read:

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Authors: apl

Last Modified:

References two_body_energies_.

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

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

private

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

inlineprotected

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

virtual

LazyEdge::prepare_for_simulated_annealing

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par Global Read:

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Authors: apl

Last Modified:

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

References ran_annealing_since_pair_energy_table_cleared_, and two_body_energies_.

Referenced by declare_energies_final_no_deletion(), and prepare_for_simulated_annealing_no_deletion().

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

inlineprotected

References prepare_for_simulated_annealing().

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

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

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

virtual

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

virtual

LazyEdge::set_sparse_aa_info

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par Global Read:

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Authors: apl

Last Modified:

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

References NOT_YET_COMPUTED_ENERGY, ran_annealing_since_pair_energy_table_cleared_, and two_body_energies_.

void core::pack::interaction_graph::LazyEdge::store_interaction_energy_first_node	(	SparseMatrixIndex const &	second_node_orig_state_sparse_info,
		int	first_node_state_offset_minus_1,
		int	second_node_curr_num_states_per_aatype,
		int	aa_neighbor_offset,
		ObjexxFCL::FArray1< core::PackerEnergy > &	edge_energy_table,
		core::PackerEnergy	interaction_energy
	)

inlinestatic

LazyEdge::store_interaction_energy_first_node

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par Global Read:

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Authors: apl

Last Modified:

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set().

Referenced by core::pack::interaction_graph::LazyNode::project_deltaE_for_substitution().

void core::pack::interaction_graph::LazyEdge::store_interaction_energy_second_node	(	SparseMatrixIndex const &	first_node_orig_state_sparse_info,
		SparseMatrixIndex const &	second_node_alternate_state_sparse_info,
		int	second_node_alt_state_num_states_per_aatype,
		int	aa_neighbor_offset,
		ObjexxFCL::FArray1< core::PackerEnergy > &	edge_energy_table,
		core::PackerEnergy	interaction_energy
	)