The double lazy interaction graph is primarily useful for multistate design where one is interested in knowing at particular edge, all of the rotamer pair energies for a particular amino acid assignment. The double lazy interaction graph is lazy in two ways: first, in delaying the computation of rotamer pair energies until they are needed, and second, in delaying the allocation of memory for rotamer pair energies until that memory is needed. The DLIG will do one of two things once it allocates space for a block of rotamer pairs: 1) In its standard operating behavior, it will leave that space allocated until the graph is destroyed, which means that the energies it stores in that block will never be computed more than once; or 2) In its alternate operating behavior, the LMIG will deallocate some of those blocks to make sure that it never uses more than some maximum amount of memory on RPEs. More...

#include <DoubleLazyInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::DoubleLazyInteractionGraph:

[legend]

Public Types
typedef OnTheFlyInteractionGraph	parent

typedef utility::pointer::shared_ptr < utility::in_place_list< int > >	InPlaceIntListOP

Public Types inherited from core::pack::interaction_graph::OnTheFlyInteractionGraph
typedef pose::Pose	Pose

typedef pose::PoseOP	PoseOP

typedef scoring::ScoreFunction	ScoreFunction

typedef scoring::ScoreFunctionOP	ScoreFunctionOP

Public Member Functions
	DoubleLazyInteractionGraph (int numNodes)

	~DoubleLazyInteractionGraph () override

void	initialize (pack_basic::RotamerSetsBase const &rot_sets) override

void	prepare_graph_for_simulated_annealing () override
	Utility signal. More...

void	blanket_assign_state_0 () override
	State initialization. More...

core::PackerEnergy	set_state_for_node (int node_ind, int new_state) override

core::PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states) override

void	consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override

core::PackerEnergy	commit_considered_substitution () override

core::PackerEnergy	get_energy_current_state_assignment () override

int	get_edge_memory_usage () const override

void	print_current_state_assignment () const override

void	set_errorfull_deltaE_threshold (core::PackerEnergy deltaE) override

core::PackerEnergy	get_energy_sum_for_vertex_group (int group_id) override

bool	aa_submatrix_energies_retrievable () const override
	Override the FixedBBInteractionGraph class's implementation of this function to return 'true'. More...

int	aatype_for_node_state (int node_ind, int node_state) const override

ObjexxFCL::FArray2D < core::PackerEnergy >	get_aa_submatrix_energies_for_edge (int node1, int node2, int node1aa, int node2aa) const override

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override

void	set_memory_max_for_rpes (int setting)

void	note_submatrix_added (int edge_index, int submatrix_index, int submatrix_size) const
	For use only from the DoubleLazyEdge; the DLE will report to the DLIG after it adds a submatrix of rotamer pair energies (that is, all the RPEs for a particular pair of amino acids) that it has done so; the DLIG monitors the access and the memory usage of the various submatrices in the graph, and may, during this function call, request that various edges (possibly the one invoking this function!) drop some of their submatrices. More...

void	note_submatrix_accessed (int edge_index, int submatrix_index) const
	For use only from the DoubleLazyEdge; the DLE will report to the DLIG after it a rotamer pair energy submatrix has been read from. The DLIG keeps track of how recently each submatrix has been accessed to ensure that, when it does ask an edge to drop a submatrix, the submatrix being dropped is the one that was accessed most distantly in the past. More...

Public Member Functions inherited from core::pack::interaction_graph::OnTheFlyInteractionGraph
	OnTheFlyInteractionGraph (int num_nodes)

	~OnTheFlyInteractionGraph () override

void	initialize (pack_basic::RotamerSetsBase const &rot_sets) override

int	get_num_aatypes () const override

bool	distinguish_backbone_and_sidechain_for_node (int node) const

void	distinguish_backbone_and_sidechain_for_node (int node, bool setting)

void	set_score_function (ScoreFunction const &)

void	set_pose (Pose const &)

Pose const &	pose () const

Pose &	non_const_pose ()
	debugging only – modify the pose during simulated annealing, if you're so inclined More...

ScoreFunction const &	score_function () const

void	zero_one_body_energy_for_node_state (int node_ind, int state)

void	add_to_one_body_energy_for_node_state (int node_ind, int state, core::PackerEnergy one_body_energy)

void	set_one_body_energy_for_node_state (int node_ind, int state, core::PackerEnergy one_body_energy)

core::PackerEnergy	get_one_body_energy_for_node_state (int node, int state) override

void	set_sparse_aa_info_for_edge (int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info)

void	reset_rpe_calculations_count ()

Size	get_num_rpe_calculations_count () const

void	note_rpe_calculated () const
	to be called by owned OTF node only More...

void	set_ProCorrection_values_for_edge (int node1, int node2, int node_not_neccessarily_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_for_edge (int node1, int node2, int node_not_neccessarily_glycine, int state, core::PackerEnergy bb_regbb_E, core::PackerEnergy bb_glybb_E, core::PackerEnergy sc_regbb_E, core::PackerEnergy sc_glybb_E)

void	note_short_range_interactions_exist_for_edge (int node1, int node2)

void	note_long_range_interactions_exist_for_edge (int node1, int node2)

unsigned int	count_dynamic_memory () const override

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

	FixedBBInteractionGraph (int num_nodes)

void	set_sparse_aa_info_for_edge (int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info)
	interface to PDEdge::set_sparse_aa_info More...

bool	get_sparse_aa_info_for_edge (int node1, int node2, int node1aa, int node2aa)
	returns true if node1aa and node2aa are amino acid neighbors More...

void	force_aa_neighbors_for_edge (int node1, int node2, int node1aa, int node2aa)
	interface to FixedBBEdge::force_aa_neighbors More...

void	force_all_aa_neighbors_for_edge (int node1, int node2)
	interface to PDEdge::force_aa_neighbors More...

virtual core::PackerEnergy	get_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2) const
	interface to FixedBBEdge::get_two_body_energy More...

Public Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase
	~InteractionGraphBase () override
	destructor More...

	InteractionGraphBase (int num_nodes)
	main constructor More...

int	get_num_nodes () const override
	Get the number of nodes in the graph. More...

void	set_num_states_for_node (int node, int num_states)
	sets the number of states for a node of a particular index NEW REQUIREMENT: Nodes must have their num-states set in ascending order by node index; that is, node 1 must go first, node 2 next, and so on. More...

int	get_num_states_for_node (int node) const override
	returns the number of states for a particular node More...

int	get_num_total_states () const override
	Get the total number of states. More...

void	add_edge (int node1, int node2)
	creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order More...

bool	get_edge_exists (int node1, int node2) const
	returns true if an edge between node1 and node2 exists More...

void	drop_all_edges_for_node (int node)
	deletes all edges adjacent to the node specified More...

void	print_vertices () const
	calls print() on each of the nodes in the graph More...

virtual void	print () const

void	output_connectivity (std::ostream &os) const
	writes out a list of all the edges in the graph More...

void	output_dimacs (std::ostream &os) const
	writes out a connectivity description of the graph in the famous dimacs format. (where the first column "DIMACS:" should be sed'ed out) More...

void	set_onebody_energies_multithreaded (core::Size const node_index, core::pack::rotamer_set::RotamerSetCOP rotset, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_assignments)
	Compute and store the onebody energy for all rotamers at a position. Safe for a multithreaded context. More...

void	prepare_graph_for_simulated_annealing () override
	iterate across edges and nodes and allow them to prepare for simulated annealing More...

void	set_edge_weight (int node1, int node2, Real edge_weight)

Real	get_edge_weight (int node1, int node2) const

bool	any_vertex_state_unassigned () const override
	Returns true if any node in the graph is in state 0, the unassigned state. More...

void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &one_body_energies)
	takes one FArray of energies – one energy for each state for each node More...

void	update_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &old_energy1b, ObjexxFCL::FArray1< core::PackerEnergy > &new_energy1b)
	decrements the one body energies by the values held in old_energy1b, increments the one body energies by the values held in new_energy1b, and copies new_energy1b into old_energy1b. More...

void	zero_one_body_energies_for_node (int node)

void	add_to_nodes_one_body_energy (int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies)

void	add_to_nodes_one_body_energy (int node_ind, ObjexxFCL::FArray1< core::PackerEnergy > const &one_body_energies)

void	add_to_nodes_one_body_energy (int node_ind, int state_id, core::PackerEnergy const one_body_energy)
	interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy More...

void	set_number_of_energy_sum_vertex_groups (int num_groups)
	a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More...

void	set_vertex_member_of_group (int vertex, int group)
	a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More...

void	print_vertex_groups ()

int	count_connected_components_and_initialize_vertex_groups ()
	makes a depth first traversal of the graph, counting the number of connected components, and initializes the vertex group memberships to reflect the connected components. Returns the number of connected components in the graph. More...

void	note_vertex_reached (int node_index)
	marks a vertex as belonging to the connected component currently being traversed in the depth first traversal. More...

bool	vertex_already_reached (int node_index)
	used by class NodeBase during the depth-first traversal to determine the number of connected components in the graph. returns true if the dft has already reached the node. More...

bool	get_vertex_member_of_energy_sum_group (int node_index, int group_id)

virtual unsigned int	getTotalMemoryUsage () const

void	reset_edge_list_iterator_for_node (int node_index) const
	set the Graph's (single) edge list iterator to the beginning of the edge list for a particular node More...

void	increment_edge_list_iterator () const
	increment the (single) edge list iterator to the next element More...

bool	edge_list_iterator_at_end () const
	test: have we arrived at the edge list end? More...

EdgeBase const &	get_edge () const
	return a const reference to an edge pointed at by the list iterator More...

virtual void	declare_all_edge_energies_final ()
	Iterates over all edges and calls declare_energies_final() on all of them. Takes O(N) time, where N is the number of edges. More...

EdgeBase const *	find_edge (int node1, int node2, bool const use_threadsafe_lookup=false) const
	Find an edge and return a const pointer to it. More...

EdgeBase *	find_edge (int node1, int node2, bool const use_threadsafe_lookup=false)
	Find an edge and return a nonconst pointer to it. More...

NodeBase *	get_node (int index) const

int	get_num_edges () const

std::list< EdgeBase * >::iterator	get_edge_list_begin ()

std::list< EdgeBase * >::iterator	get_edge_list_end ()

std::list< EdgeBase * > ::const_iterator	get_edge_list_begin () const

std::list< EdgeBase * > ::const_iterator	get_edge_list_end () const

Public Member Functions inherited from core::pack::interaction_graph::AnnealableGraphBase
	AnnealableGraphBase ()
	Constructor. More...

	AnnealableGraphBase (AnnealableGraphBase const &src)
	Copy constructor. More...

	~AnnealableGraphBase () override
	Destructor. More...

virtual void	clean_up_after_packing (core::pose::Pose &pose)
	Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing. More...

Protected Member Functions
NodeBase *	create_new_node (int node_index, int num_states) override

EdgeBase *	create_new_edge (int index1, int index2) override

core::PackerEnergy	get_energy_PD_current_state_assignment ()

void	update_internal_energy_totals ()

DoubleLazyNode const *	get_dlazy_node (int index) const

DoubleLazyNode *	get_dlazy_node (int index)

DoubleLazyEdge const *	get_dlazy_edge (int node1, int node2) const

DoubleLazyEdge *	get_dlazy_edge (int node1, int node2)

Protected Member Functions inherited from core::pack::interaction_graph::OnTheFlyInteractionGraph
OnTheFlyNode *	get_on_the_fly_node (int node_index)

OnTheFlyNode const *	get_on_the_fly_node (int node_index) const

Protected Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph
FixedBBNode const *	get_fixedbb_node (int node_index) const
	Downcasts. More...

FixedBBNode *	get_fixedbb_node (int node_index)

FixedBBEdge const *	get_fixedbb_edge (int node1, int node2) const

FixedBBEdge *	get_fixedbb_edge (int node1, int node2)

Protected Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase
void	clean_up_edges_marked_for_deletion ()
	Remove those edges that have marked themselves for deletion. More...

void	drop_edge (std::list< EdgeBase * >::iterator edge)
	removes edge from edge list at iterator iter More...

int	get_node_state_offset (int index) const

bool	mine (EdgeBase const *edge) const

Private Member Functions
	DoubleLazyInteractionGraph ()

	DoubleLazyInteractionGraph (DoubleLazyInteractionGraph const &)

DoubleLazyInteractionGraph &	operator= (DoubleLazyInteractionGraph const &)

Private Attributes
int	sqr_num_aa_types_

int	num_commits_since_last_update_

core::PackerEnergy	total_energy_current_state_assignment_

core::PackerEnergy	total_energy_alternate_state_assignment_

int	node_considering_alt_state_

int	memory_max_for_rpes_

int	curr_memory_for_rpes_

utility::vector0 < DoubleLazyEdge * >	dlazy_edge_vector_
	initialized in prepare_for_simulated_annealing(); More...

InPlaceIntListOP	aa_submatrix_history_list_

Static Private Attributes
static const int	COMMIT_LIMIT_BETWEEN_UPDATES = 1024

Detailed Description

The double lazy interaction graph is primarily useful for multistate design where one is interested in knowing at particular edge, all of the rotamer pair energies for a particular amino acid assignment. The double lazy interaction graph is lazy in two ways: first, in delaying the computation of rotamer pair energies until they are needed, and second, in delaying the allocation of memory for rotamer pair energies until that memory is needed. The DLIG will do one of two things once it allocates space for a block of rotamer pairs: 1) In its standard operating behavior, it will leave that space allocated until the graph is destroyed, which means that the energies it stores in that block will never be computed more than once; or 2) In its alternate operating behavior, the LMIG will deallocate some of those blocks to make sure that it never uses more than some maximum amount of memory on RPEs.

Member Typedef Documentation

typedef utility::pointer::shared_ptr< utility::in_place_list< int > > core::pack::interaction_graph::DoubleLazyInteractionGraph::InPlaceIntListOP

typedef OnTheFlyInteractionGraph core::pack::interaction_graph::DoubleLazyInteractionGraph::parent

Constructor & Destructor Documentation

core::pack::interaction_graph::DoubleLazyInteractionGraph::DoubleLazyInteractionGraph ( int numNodes )

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

core::pack::interaction_graph::DoubleLazyInteractionGraph::~DoubleLazyInteractionGraph ( )

override

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References core::pack::interaction_graph::DoubleLazyEdge::actual_twobody_memory_use(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), and core::pack::interaction_graph::DoubleLazyEdge::potential_twobody_memory_use().

core::pack::interaction_graph::DoubleLazyInteractionGraph::DoubleLazyInteractionGraph ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

bool core::pack::interaction_graph::DoubleLazyInteractionGraph::aa_submatrix_energies_retrievable ( ) const

overridevirtual

Override the FixedBBInteractionGraph class's implementation of this function to return 'true'.

DoubleLazyInteractionGraph will return aa submatrices as requested.

Reimplemented from core::pack::interaction_graph::FixedBBInteractionGraph.

int core::pack::interaction_graph::DoubleLazyInteractionGraph::aatype_for_node_state	(	int	node_ind,
		int	node_state
	)		const

overridevirtual

Derived classes wishing to respond to the get_aa_submatrix_energies_for_edge must implement this function as well, which allows the mapping between states and their on-node amino-acid index (which may very well represent something other than the index of the enumeration element for the rotamer's "aa()").

Reimplemented from core::pack::interaction_graph::FixedBBInteractionGraph.

References core::pack::interaction_graph::DoubleLazyNode::aatype_for_state(), and get_dlazy_node().

void core::pack::interaction_graph::DoubleLazyInteractionGraph::blanket_assign_state_0 ( )

overridevirtual

State initialization.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleLazyNode::assign_zero_state(), get_dlazy_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), and total_energy_current_state_assignment_.

core::PackerEnergy core::pack::interaction_graph::DoubleLazyInteractionGraph::commit_considered_substitution ( )

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleLazyNode::commit_considered_substitution(), COMMIT_LIMIT_BETWEEN_UPDATES, get_dlazy_node(), node_considering_alt_state_, num_commits_since_last_update_, total_energy_alternate_state_assignment_, total_energy_current_state_assignment_, and update_internal_energy_totals().

void core::pack::interaction_graph::DoubleLazyInteractionGraph::consider_substitution	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_energy_for_node
	)

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References get_dlazy_node(), node_considering_alt_state_, total_energy_alternate_state_assignment_, and total_energy_current_state_assignment_.

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

overridevirtual

Reimplemented from core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::OnTheFlyInteractionGraph::count_dynamic_memory().

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

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References DoubleLazyInteractionGraph().

EdgeBase * core::pack::interaction_graph::DoubleLazyInteractionGraph::create_new_edge	(	int	index1,
		int	index2
	)

overrideprotectedvirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

NodeBase * core::pack::interaction_graph::DoubleLazyInteractionGraph::create_new_node	(	int	node_index,
		int	num_states
	)

overrideprotectedvirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

ObjexxFCL::FArray2D< core::PackerEnergy > core::pack::interaction_graph::DoubleLazyInteractionGraph::get_aa_submatrix_energies_for_edge	(	int	node1,
		int	node2,
		int	node1aa,
		int	node2aa
	)		const

overridevirtual

Do not call this function unless it is implemented in the derived class, as should be indicated by the "aa_submatrix_energies_retrivable" method.

Reimplemented from core::pack::interaction_graph::FixedBBInteractionGraph.

References core::pack::interaction_graph::DoubleLazyEdge::get_aa_submatrix_energies(), and get_dlazy_edge().

DoubleLazyEdge const* core::pack::interaction_graph::DoubleLazyInteractionGraph::get_dlazy_edge	(	int	node1,
		int	node2
	)		const

inlineprotected

References core::pack::interaction_graph::InteractionGraphBase::find_edge().

Referenced by get_aa_submatrix_energies_for_edge().

DoubleLazyEdge* core::pack::interaction_graph::DoubleLazyInteractionGraph::get_dlazy_edge	(	int	node1,
		int	node2
	)

inlineprotected

References core::pack::interaction_graph::InteractionGraphBase::find_edge().

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

inlineprotected

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

Referenced by aatype_for_node_state(), blanket_assign_state_0(), commit_considered_substitution(), consider_substitution(), get_energy_sum_for_vertex_group(), print_current_state_assignment(), set_network_state(), set_state_for_node(), and update_internal_energy_totals().

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

inlineprotected

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

int core::pack::interaction_graph::DoubleLazyInteractionGraph::get_edge_memory_usage ( ) const

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), and core::simple_metrics::metrics::sum.

core::PackerEnergy core::pack::interaction_graph::DoubleLazyInteractionGraph::get_energy_current_state_assignment ( )

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References total_energy_current_state_assignment_, and update_internal_energy_totals().

core::PackerEnergy core::pack::interaction_graph::DoubleLazyInteractionGraph::get_energy_PD_current_state_assignment ( )

protected

References total_energy_current_state_assignment_.

core::PackerEnergy core::pack::interaction_graph::DoubleLazyInteractionGraph::get_energy_sum_for_vertex_group ( int group_id )

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References get_dlazy_node(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), core::pack::interaction_graph::DoubleLazyNode::get_one_body_energy_current_state(), and core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group().

void core::pack::interaction_graph::DoubleLazyInteractionGraph::initialize ( pack_basic::RotamerSetsBase const & rot_sets )

overridevirtual

Implements core::pack::interaction_graph::InteractionGraphBase.

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

void core::pack::interaction_graph::DoubleLazyInteractionGraph::note_submatrix_accessed	(	int	edge_index,
		int	submatrix_index
	)		const

For use only from the DoubleLazyEdge; the DLE will report to the DLIG after it a rotamer pair energy submatrix has been read from. The DLIG keeps track of how recently each submatrix has been accessed to ensure that, when it does ask an edge to drop a submatrix, the submatrix being dropped is the one that was accessed most distantly in the past.

References aa_submatrix_history_list_, memory_max_for_rpes_, and sqr_num_aa_types_.

Referenced by core::pack::interaction_graph::DoubleLazyEdge::get_aa_submatrix_energies(), and note_submatrix_added().

void core::pack::interaction_graph::DoubleLazyInteractionGraph::note_submatrix_added	(	int	edge_index,
		int	submatrix_index,
		int	submatrix_size
	)		const

For use only from the DoubleLazyEdge; the DLE will report to the DLIG after it adds a submatrix of rotamer pair energies (that is, all the RPEs for a particular pair of amino acids) that it has done so; the DLIG monitors the access and the memory usage of the various submatrices in the graph, and may, during this function call, request that various edges (possibly the one invoking this function!) drop some of their submatrices.

References aa_submatrix_history_list_, curr_memory_for_rpes_, dlazy_edge_vector_, memory_max_for_rpes_, note_submatrix_accessed(), and sqr_num_aa_types_.

Referenced by core::pack::interaction_graph::DoubleLazyEdge::prep_aa_submatrix().

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

private

void core::pack::interaction_graph::DoubleLazyInteractionGraph::prepare_graph_for_simulated_annealing ( )

overridevirtual

Utility signal.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References aa_submatrix_history_list_, dlazy_edge_vector_, core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_edges(), memory_max_for_rpes_, core::pack::interaction_graph::InteractionGraphBase::prepare_graph_for_simulated_annealing(), core::pack::interaction_graph::DoubleLazyEdge::set_edge_index(), and sqr_num_aa_types_.

void core::pack::interaction_graph::DoubleLazyInteractionGraph::print_current_state_assignment ( ) const

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleLazyNode::get_current_state(), get_dlazy_node(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), core::pack::interaction_graph::DoubleLazyNode::print(), and total_energy_current_state_assignment_.

void core::pack::interaction_graph::DoubleLazyInteractionGraph::set_errorfull_deltaE_threshold ( core::PackerEnergy deltaE )

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

void core::pack::interaction_graph::DoubleLazyInteractionGraph::set_memory_max_for_rpes ( int setting )

References memory_max_for_rpes_.

core::PackerEnergy core::pack::interaction_graph::DoubleLazyInteractionGraph::set_network_state ( ObjexxFCL::FArray1_int & node_states )

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleLazyNode::complete_state_assignment(), get_dlazy_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), core::pack::interaction_graph::DoubleLazyNode::partial_assign_state(), total_energy_current_state_assignment_, and update_internal_energy_totals().

core::PackerEnergy core::pack::interaction_graph::DoubleLazyInteractionGraph::set_state_for_node	(	int	node_ind,
		int	new_state
	)

overridevirtual

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::InteractionGraphBase.

References core::pack::interaction_graph::DoubleLazyNode::assign_state(), get_dlazy_node(), total_energy_current_state_assignment_, and update_internal_energy_totals().

void core::pack::interaction_graph::DoubleLazyInteractionGraph::update_internal_energy_totals ( )

protected

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References get_dlazy_node(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), num_commits_since_last_update_, and total_energy_current_state_assignment_.

Referenced by commit_considered_substitution(), get_energy_current_state_assignment(), set_network_state(), and set_state_for_node().

Member Data Documentation

InPlaceIntListOP core::pack::interaction_graph::DoubleLazyInteractionGraph::aa_submatrix_history_list_

mutableprivate

Referenced by note_submatrix_accessed(), note_submatrix_added(), and prepare_graph_for_simulated_annealing().

const int core::pack::interaction_graph::DoubleLazyInteractionGraph::COMMIT_LIMIT_BETWEEN_UPDATES = 1024

staticprivate

Referenced by commit_considered_substitution().

int core::pack::interaction_graph::DoubleLazyInteractionGraph::curr_memory_for_rpes_

mutableprivate

Referenced by note_submatrix_added().

utility::vector0< DoubleLazyEdge * > core::pack::interaction_graph::DoubleLazyInteractionGraph::dlazy_edge_vector_

private

initialized in prepare_for_simulated_annealing();

Referenced by note_submatrix_added(), and prepare_graph_for_simulated_annealing().

int core::pack::interaction_graph::DoubleLazyInteractionGraph::memory_max_for_rpes_

private

Referenced by note_submatrix_accessed(), note_submatrix_added(), prepare_graph_for_simulated_annealing(), and set_memory_max_for_rpes().

int core::pack::interaction_graph::DoubleLazyInteractionGraph::node_considering_alt_state_

private

Referenced by commit_considered_substitution(), and consider_substitution().

int core::pack::interaction_graph::DoubleLazyInteractionGraph::num_commits_since_last_update_

private

Referenced by commit_considered_substitution(), and update_internal_energy_totals().

int core::pack::interaction_graph::DoubleLazyInteractionGraph::sqr_num_aa_types_

private

Referenced by initialize(), note_submatrix_accessed(), note_submatrix_added(), and prepare_graph_for_simulated_annealing().

core::PackerEnergy core::pack::interaction_graph::DoubleLazyInteractionGraph::total_energy_alternate_state_assignment_

private

Referenced by commit_considered_substitution(), and consider_substitution().

core::PackerEnergy core::pack::interaction_graph::DoubleLazyInteractionGraph::total_energy_current_state_assignment_

private

Referenced by blanket_assign_state_0(), commit_considered_substitution(), consider_substitution(), get_energy_current_state_assignment(), get_energy_PD_current_state_assignment(), print_current_state_assignment(), set_network_state(), set_state_for_node(), and update_internal_energy_totals().

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

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

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