#include <PDInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::PDEdge:

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

	~PDEdge () override
	destructor More...

void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &sparse_conn_info) override
	allocates two-body energy table based on amino-acid neighbor relationships and initializes the table to 0. More...

void	force_aa_neighbors (int node1aa, int node2aa) override
	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...

void	force_all_aa_neighbors () override
	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...

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

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 so long as the amion acid types of those states have been previously declared amino acid neighbors. Any energies for non-neighboring states are ignored. 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	declare_energies_final () override
	When all the energies that are going to be stored in an edge have been placed in it, the edge may save some memory by shrinking its AminoAcidNeighborSparseMatrix. This method instructs the edge to do so. More...

void	prepare_for_simulated_annealing () override
	reduces the size of the pair-energy table if any amino-acid-neighbor submatrices hold nothing but 0's 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, SparseMatrixIndex const &new_state_sparse_info, 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, SparseMatrixIndex const &nodes_new_state_sparse_info)
	update bookkeeping information when one of the nodes an edge is incident upon changes state More...

ObjexxFCL::FArray2D_int const &	get_offsets_for_aatypes ()
	Returns the array of offsets into the sparse two-body energy table for amino-acid neighbors. Used in transferring information from edges onto nodes for cache efficiency. More...

utility::vector1< int > const &	get_second_node_num_states_per_aa ()
	returns an FArray of the number of states for each amino acid type for the higher-indexed node More...

int	get_two_body_table_size () const
	returns the memory usage of the two body energy table for this edge More...

core::PackerEnergy &	get_edge_table_ptr ()
	Returns a reference to the first element in the sparse two-body energy table. Used to create a proxy array on the nodes for cache efficiency. More...

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override

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

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

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 method that looks up the two body energy when the node with the larger index on an edge is considering an alternate state More...

Protected Member Functions
void	declare_energies_final_no_deletion ()
	allow derived class to prep this class for simA, but guarantee no call to delete this; More...

void	prepare_for_simulated_annealing_no_deletion ()
	allow derived class to prep this class for simA, but guarantee no call to delete this; More...

bool	pd_edge_table_all_zeros () const
	if edge table is empty, returns true – assumes prepare_for_simulated_annealing_no_deletion() has been called first. More...

AminoAcidNeighborSparseMatrix < core::PackerEnergy > &	two_body_energies ()

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
PDNode const *	get_pd_node (int index) const

PDNode *	get_pd_node (int index)

PDInteractionGraph const *	get_pdig_owner () const

PDInteractionGraph *	get_pdig_owner ()

void	drop_small_submatrices_where_possible (core::PackerEnergy epsilon)
	drops any amino-acid neighbor submatrix of the two-body energy table when the magnitudes of the energies stored in that submatrix do not exceed the input parameter, epsilon. Dropping submatrices that contain zero energies is a special case of this function where epsilon == 0. More...

void	drop_zero_submatrices_where_possible ()
	drops amino-acid neighbor submatrices when they do not contain any non-zero entries. Represents a special case of drop_small_submatrices_where_possible More...

	PDEdge ()

	PDEdge (PDEdge const &)

PDEdge &	operator= (PDEdge const &)

Private Attributes
AminoAcidNeighborSparseMatrix < core::PackerEnergy >	two_body_energies_

core::PackerEnergy	curr_state_energy_

bool	energies_updated_since_last_prep_for_simA_

Constructor & Destructor Documentation

core::pack::interaction_graph::PDEdge::PDEdge	(	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

References force_all_aa_neighbors().

core::pack::interaction_graph::PDEdge::~PDEdge ( )

overridedefault

destructor

core::pack::interaction_graph::PDEdge::PDEdge ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

void core::pack::interaction_graph::PDEdge::acknowledge_state_change	(	int	node_ind,
		int	new_state,
		SparseMatrixIndex const &	new_state_sparse_info,
		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_state_spare_info	- [in] - the sparse-matrix information for the state
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::PDNode::assign_state().

void core::pack::interaction_graph::PDEdge::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 curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), get_pd_node(), 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::PDEdge::acknowledge_substitution	(	int	substituted_node_index,
		core::PackerEnergy const	curr_state_energy,
		int	nodes_new_state,
		SparseMatrixIndex const &	nodes_new_state_sparse_info
	)

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_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), and get_pd_node().

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

void core::pack::interaction_graph::PDEdge::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::PDEdge::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 so long as the amion acid types of those states have been previously declared amino acid neighbors. Any energies for non-neighboring states are ignored.

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

void core::pack::interaction_graph::PDEdge::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::PDEdge::count_dynamic_memory ( ) const

overridevirtual

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

References core::pack::interaction_graph::EdgeBase::count_dynamic_memory(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_offset_table_size_in_bytes(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_table_size(), and two_body_energies_.

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

overridevirtual

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

References PDEdge().

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

overridevirtual

When all the energies that are going to be stored in an edge have been placed in it, the edge may save some memory by shrinking its AminoAcidNeighborSparseMatrix. This method instructs the edge to do so.

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

References prepare_for_simulated_annealing().

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

protected

allow derived class to prep this class for simA, but guarantee no call to delete this;

References prepare_for_simulated_annealing_no_deletion().

void core::pack::interaction_graph::PDEdge::drop_small_submatrices_where_possible ( core::PackerEnergy epsilon )

private

drops any amino-acid neighbor submatrix of the two-body energy table when the magnitudes of the energies stored in that submatrix do not exceed the input parameter, epsilon. Dropping submatrices that contain zero energies is a special case of this function where epsilon == 0.

Parameters

epsilon - [in] - the magnitude threshold for keeping amino-acid neighbor submatrices.

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::drop_small_submatrices_where_possible(), and two_body_energies_.

Referenced by drop_zero_submatrices_where_possible().

void core::pack::interaction_graph::PDEdge::drop_zero_submatrices_where_possible ( )

private

drops amino-acid neighbor submatrices when they do not contain any non-zero entries. Represents a special case of drop_small_submatrices_where_possible

References drop_small_submatrices_where_possible().

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

overridevirtual

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 energies_updated_since_last_prep_for_simA_, core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::force_aa_neighbors(), and two_body_energies_.

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

overridevirtual

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 energies_updated_since_last_prep_for_simA_, core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::force_all_aa_neighbors(), and two_body_energies_.

Referenced by core::pack::interaction_graph::PDInteractionGraph::add_edge(), and PDEdge().

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

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_aa_submatrix_energies(), and two_body_energies_.

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

float core::pack::interaction_graph::PDEdge::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

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
second_node_orig_state_sparse_info	- [in] - the sparse matrix info for the higher-indexed node
first_node_state_offset_minus_1	- [in] - part of the sparse matrix info for the lower-indexed node where 1 is subtracted from the state offset.
second_node_num_states_per_aatype	- [in] - number of states with current aa type for node 2
aa_neighbor_offset	- [in] - offset for the amino-acid neighbor pair for the sparse two-body energy table
edge_energy_table	- [in] - the proxy FArray pointing at the edge table connecting the two nodes.

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

float core::pack::interaction_graph::PDEdge::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

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

Parameters

first_node_orig_state	- [in] - the current state for the lower-indexed node
second_node_alt_state	- [in] - the alt state for the higher-indexed node
first_node_orig_state_sparse_info	- [in] - the sparse matrix info for the lower-indexed node
second_node_alt_state_sparse_info	- [in] - the sparse matrix info for the higher-indexed node
first_node_state_offset_minus_1	- [in] - part of the sparse matrix info for the lower-indexed node where 1 is subtracted from the state offset.
second_node_alt_state_num_states_per_aatype	- [in] - number of states with alternate aa type for node 2
aa_neighbor_offset	- [in] - offset for the amino-acid neighbor pair for the sparse two-body energy table
edge_energy_table	- [in] - the proxy FArray pointing at the edge table connecting the two nodes.

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

float core::pack::interaction_graph::PDEdge::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::PDNode::update_internal_energy_sums().

float & core::pack::interaction_graph::PDEdge::get_edge_table_ptr ( )

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

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::getMatrixPointer(), and two_body_energies_.

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

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

Returns the array of offsets into the sparse two-body energy table for amino-acid neighbors. Used in transferring information from edges onto nodes for cache efficiency.

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::getAANeighborOffsets(), and two_body_energies_.

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

PDNode const * core::pack::interaction_graph::PDEdge::get_pd_node ( int index ) const

inlineprivate

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

Referenced by acknowledge_state_zeroed(), acknowledge_substitution(), get_second_node_num_states_per_aa(), and get_two_body_energy().

PDNode * core::pack::interaction_graph::PDEdge::get_pd_node ( int index )

inlineprivate

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

PDInteractionGraph const * core::pack::interaction_graph::PDEdge::get_pdig_owner ( ) const

inlineprivate

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

PDInteractionGraph * core::pack::interaction_graph::PDEdge::get_pdig_owner ( )

inlineprivate

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

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

returns an FArray of the number of states for each amino acid type for the higher-indexed node

References core::pack::interaction_graph::PDNode::get_num_states_for_aa_types(), and get_pd_node().

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

bool core::pack::interaction_graph::PDEdge::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 core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_sparse_aa_info(), and two_body_energies_.

float core::pack::interaction_graph::PDEdge::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 core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get(), get_pd_node(), and two_body_energies_.

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

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

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_table_size(), and two_body_energies_.

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

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

private

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

protected

if edge table is empty, returns true – assumes prepare_for_simulated_annealing_no_deletion() has been called first.

References energies_updated_since_last_prep_for_simA_, core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_table_size(), and two_body_energies_.

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

overridevirtual

reduces the size of the pair-energy table if any amino-acid-neighbor submatrices hold nothing but 0's

since the drop_zero_submatrices_where_possible() method of the AANSM is somewhat time consuming, and since it can only reduce memory use / simA running time on the first execution following an update to the two-body energies, the PDEdge member variable energies_updated_since_last_prep_ for_simA ensures that the AANSM method is only called once following the update of any RPEs.

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

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_table_size(), core::pack::interaction_graph::EdgeBase::mark_edge_for_deletion(), prepare_for_simulated_annealing_no_deletion(), and two_body_energies_.

Referenced by declare_energies_final().

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

protected

allow derived class to prep this class for simA, but guarantee no call to delete this;

References core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::drop_zero_submatrices_where_possible(), energies_updated_since_last_prep_for_simA_, and two_body_energies_.

Referenced by declare_energies_final_no_deletion(), and prepare_for_simulated_annealing().

void core::pack::interaction_graph::PDEdge::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, one would have to worry about its data integrity as well. General advice: don't change energies during simA.

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

References core::pack::interaction_graph::EdgeBase::edge_weight(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::scale(), and two_body_energies_.

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

overridevirtual

allocates two-body energy table based on amino-acid neighbor relationships and initializes the table to 0.

Parameters

sparse_conn_info - [in] - a MAX_AA x MAX_AA 2D array where each "true" entry means that the corresponding amino acid pair are neighbors.

Remarks: idea borrowed from energy2b implementation

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

References energies_updated_since_last_prep_for_simA_, core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set_sparse_aa_info(), and two_body_energies_.

void core::pack::interaction_graph::PDEdge::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.

AminoAcidNeighborSparseMatrix< core::PackerEnergy >& core::pack::interaction_graph::PDEdge::two_body_energies ( )

inlineprotected

References two_body_energies_.

Referenced by core::pack::hbonds::BareMinimumPDEdge::BareMinimumPDEdge().