core::pack::interaction_graph::DoubleLazyEdge Class Reference

#include <DoubleLazyInteractionGraph.hh>

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

Collaboration diagram for core::pack::interaction_graph::DoubleLazyEdge:

Public Member Functions
	DoubleLazyEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
virtual	~DoubleLazyEdge ()
virtual void	set_sparse_aa_info (FArray2_bool const &)
virtual void	force_aa_neighbors (int node1aa, int node2aa)
virtual void	force_all_aa_neighbors ()
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
core::PackerEnergy	get_two_body_energy_smi (int const node1state, int const node2state, SparseMatrixIndex const &node1info, SparseMatrixIndex const &node2info) 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)
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
virtual unsigned int	count_static_memory () const
virtual unsigned int	count_dynamic_memory () const
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
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)
virtual void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &sparse_conn_info)=0
Public Member Functions inherited from core::pack::interaction_graph::EdgeBase
virtual	~EdgeBase ()
	copy constructor, do not use More...
	EdgeBase (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
	main constructor for edge, no default nor copy constructors More...
int	get_other_ind (int callers_index) const
	returns the index of the other node that the edge is incident upon More...
NodeBase *	get_other_node (int callers_index) const
	returns a pointer to the other node that the edge is incident upon More...
int	get_first_node_ind () const
	returns the index of the smaller-indexed node More...
int	get_second_node_ind () const
	returns the index of the larger-indexed node More...
void	set_pos_in_owners_list (std::list< EdgeBase * >::iterator edge_iterator)
	edge keeps iterator to its position in it's owner's edge list More...
void	set_pos_in_node_edgevector (int callers_index, int position)
	edge keeps index it has in node_ind's edge vector More...
bool	same_edge (int node1, int node2) const
	returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important More...
Real	edge_weight () const
InteractionGraphBase const *	get_owner () const
InteractionGraphBase *	get_owner ()

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

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)

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_

Detailed Description

Definition at line 191 of file DoubleLazyInteractionGraph.hh.

Constructor & Destructor Documentation

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

DoubleLazyEdge::DoubleLazyEdge

Detailed:

Parameters

@par	Global Read:

Global Write:

Remarks

References:

Authors

apl

Last Modified:

Definition at line 618 of file DoubleLazyInteractionGraph.cc.

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

virtual

explicity deallocate the FArrays that were dynamically allocated

Definition at line 643 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 1248 of file DoubleLazyInteractionGraph.cc.

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
	)

DoubleLazyEdge::acknowledge_partial_state_change

Detailed:

Parameters

@par	Global Read:

Global Write:

Remarks

References:

Authors

apl

Last Modified:

Definition at line 1036 of file DoubleLazyInteractionGraph.cc.

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
	)

DoubleLazyEdge::acknowledge_state_change

Detailed:

Parameters

@par	Global Read:

Global Write:

Remarks

References:

Authors

apl

Last Modified:

Definition at line 939 of file DoubleLazyInteractionGraph.cc.

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)

DoubleLazyEdge::acknowledge_state_zeroed

Detailed:

Parameters

@par	Global Read:

Global Write:

Remarks

References:

Authors

apl

Last Modified:

Definition at line 996 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 609 of file DoubleLazyInteractionGraph.hh.

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

Definition at line 813 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 283 of file DoubleLazyInteractionGraph.hh.

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

virtual

add up all the submatrices

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

Definition at line 794 of file DoubleLazyInteractionGraph.cc.

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

virtual

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

Definition at line 787 of file DoubleLazyInteractionGraph.cc.

References DoubleLazyEdge().

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

virtual

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

Definition at line 767 of file DoubleLazyInteractionGraph.cc.

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

inlineprotected

Definition at line 326 of file DoubleLazyInteractionGraph.hh.

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.

Definition at line 858 of file DoubleLazyInteractionGraph.cc.

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  )

virtual

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

Definition at line 676 of file DoubleLazyInteractionGraph.cc.

References sparse_aa_neighbors_.

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

virtual

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

Definition at line 681 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 1167 of file DoubleLazyInteractionGraph.cc.

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

DoubleLazyEdge::get_current_two_body_energy

Detailed:

Parameters

@par	Global Read:

Global Write:

Remarks

References:

Authors

apl

Last Modified:

Definition at line 912 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 596 of file DoubleLazyInteractionGraph.hh.

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

Definition at line 602 of file DoubleLazyInteractionGraph.hh.

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

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

inlineprivate

Definition at line 584 of file DoubleLazyInteractionGraph.hh.

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

Definition at line 590 of file DoubleLazyInteractionGraph.hh.

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

core::PackerEnergy core::pack::interaction_graph::DoubleLazyEdge::get_energy_following_partial_state_assignment

(

)

DoubleLazyEdge::get_energy_following_partial_state_assignment

Detailed:

Parameters

@par	Global Read:

Global Write:

Remarks

References:

Authors

apl

Last Modified:

Definition at line 1078 of file DoubleLazyInteractionGraph.cc.

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

DoubleLazyEdge::get_energy_for_state_pair

Detailed:

Parameters

@par	Global Read:

Global Write:

Remarks

References:

Authors

apl

Last Modified:

Definition at line 1146 of file DoubleLazyInteractionGraph.cc.

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

virtual

returns whether two amino acid types are represented as neighbors

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

Definition at line 671 of file DoubleLazyInteractionGraph.cc.

References sparse_aa_neighbors_.

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

virtual

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

Definition at line 687 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 698 of file DoubleLazyInteractionGraph.cc.

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

DoubleLazyEdge::get_two_body_table_size

Detailed:

Parameters

@par	Global Read:

Global Write:

Remarks

References:

Authors

apl

Last Modified:

Definition at line 1118 of file DoubleLazyInteractionGraph.cc.

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

private

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

inlineprotected

Definition at line 328 of file DoubleLazyInteractionGraph.hh.

unsigned int core::pack::interaction_graph::DoubleLazyEdge::potential_twobody_memory_use

(

)

const

Definition at line 828 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 722 of file DoubleLazyInteractionGraph.cc.

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 ( )

virtual

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

Definition at line 771 of file DoubleLazyInteractionGraph.cc.

References 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

Definition at line 327 of file DoubleLazyInteractionGraph.hh.

References prepare_for_simulated_annealing().

void core::pack::interaction_graph::DoubleLazyEdge::print_current_energy

(

)

const

Definition at line 1227 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 742 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 755 of file DoubleLazyInteractionGraph.cc.

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.

Definition at line 849 of file DoubleLazyInteractionGraph.cc.

References edge_index_.

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

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

virtual

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

Definition at line 870 of file DoubleLazyInteractionGraph.cc.

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 ( FArray2_bool const &  aa_neighbors)

virtual

Definition at line 653 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 1235 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 1241 of file DoubleLazyInteractionGraph.cc.

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

Definition at line 380 of file DoubleLazyInteractionGraph.hh.

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

Definition at line 388 of file DoubleLazyInteractionGraph.hh.

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

Definition at line 294 of file DoubleLazyInteractionGraph.hh.

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

Definition at line 381 of file DoubleLazyInteractionGraph.hh.

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

Definition at line 382 of file DoubleLazyInteractionGraph.hh.

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

Definition at line 375 of file DoubleLazyInteractionGraph.hh.

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.

Definition at line 379 of file DoubleLazyInteractionGraph.hh.

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().

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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