#include <LinearMemoryInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::LinearMemoryInteractionGraph:

Collaboration diagram for core::pack::interaction_graph::LinearMemoryInteractionGraph:

Public Member Functions
	LinearMemoryInteractionGraph (int numNodes)

virtual	~LinearMemoryInteractionGraph ()

virtual void	blanket_assign_state_0 ()

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

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

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

virtual core::PackerEnergy	commit_considered_substitution ()

virtual core::PackerEnergy	get_energy_current_state_assignment ()

virtual int	get_edge_memory_usage () const

virtual void	print_current_state_assignment () const

virtual void	set_errorfull_deltaE_threshold (core::PackerEnergy deltaE)

virtual core::PackerEnergy	get_energy_sum_for_vertex_group (int group_id)

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

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

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

	~OnTheFlyInteractionGraph ()

virtual void	initialize (rotamer_set::RotamerSetsBase const &rot_sets)

int	get_num_aatypes () const

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)

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

void	set_sparse_aa_info_for_edge (int node1, int node2, 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_nonprobb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_nonprobb_E, core::PackerEnergy sc_probb_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)

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

	FixedBBInteractionGraph (int num_nodes)

virtual bool	aa_submatrix_energies_retrievable () const

virtual int	aatype_for_node_state (int node_ind, int node_state) const

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

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
virtual	~InteractionGraphBase ()
	destructor More...

	InteractionGraphBase (int num_nodes)
	main constructor More...

virtual int	get_num_nodes_v () const

int	get_num_nodes () const

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
	returns the number of states for a particular node More...

int	get_num_total_states () const

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)
	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_edge_weight (int node1, int node2, Real edge_weight)

Real	get_edge_weight (int node1, int node2) const

bool	any_vertex_state_unassigned () const
	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...

EdgeBase const *	find_edge (int node1, int node2) const
	returns the edge connecting node1 and node2 More...

EdgeBase *	find_edge (int node1, int node2)

NodeBase *	get_node (int index) const

int	get_num_edges () const

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

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

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

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

virtual EdgeBase *	create_new_edge (int index1, int index2)

core::PackerEnergy	get_energy_PD_current_state_assignment ()
	O(1) total energy report. Protected read access for derived classes. More...

void	update_internal_energy_totals ()

LinearMemNode const *	get_linmem_node (int index) const

LinearMemNode *	get_linmem_node (int index)

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	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
void	set_recent_history_sizes ()

	LinearMemoryInteractionGraph ()

	LinearMemoryInteractionGraph (LinearMemoryInteractionGraph const &)

LinearMemoryInteractionGraph &	operator= (LinearMemoryInteractionGraph const &)

Private Attributes
bool	first_time_prepping_for_simA_

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_

bool	have_not_committed_last_substitution_

Static Private Attributes
static const int	COMMIT_LIMIT_BETWEEN_UPDATES = 1024

Additional Inherited Members
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

Detailed Description

Definition at line 374 of file LinearMemoryInteractionGraph.hh.

Constructor & Destructor Documentation

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

Definition at line 1228 of file LinearMemoryInteractionGraph.cc.

core::pack::interaction_graph::LinearMemoryInteractionGraph::~LinearMemoryInteractionGraph ( )

virtual

Definition at line 1241 of file LinearMemoryInteractionGraph.cc.

core::pack::interaction_graph::LinearMemoryInteractionGraph::LinearMemoryInteractionGraph ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

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

virtual

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

Definition at line 1245 of file LinearMemoryInteractionGraph.cc.

References core::pack::interaction_graph::LinearMemNode::assign_zero_state(), get_linmem_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), have_not_committed_last_substitution_, and total_energy_current_state_assignment_.

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

virtual

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

Definition at line 1312 of file LinearMemoryInteractionGraph.cc.

References core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), COMMIT_LIMIT_BETWEEN_UPDATES, get_linmem_node(), have_not_committed_last_substitution_, 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::LinearMemoryInteractionGraph::consider_substitution	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_energy_for_node
	)

virtual

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

Definition at line 1288 of file LinearMemoryInteractionGraph.cc.

References get_linmem_node(), have_not_committed_last_substitution_, node_considering_alt_state_, total_energy_alternate_state_assignment_, and total_energy_current_state_assignment_.

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

virtual

Reimplemented from core::pack::interaction_graph::OnTheFlyInteractionGraph.

Definition at line 1430 of file LinearMemoryInteractionGraph.cc.

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

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

virtual

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

Definition at line 1424 of file LinearMemoryInteractionGraph.cc.

References LinearMemoryInteractionGraph().

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

protectedvirtual

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

Definition at line 1445 of file LinearMemoryInteractionGraph.cc.

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

protectedvirtual

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

Definition at line 1438 of file LinearMemoryInteractionGraph.cc.

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

virtual

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

Definition at line 1346 of file LinearMemoryInteractionGraph.cc.

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

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

virtual

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

Definition at line 1331 of file LinearMemoryInteractionGraph.cc.

References total_energy_current_state_assignment_, and update_internal_energy_totals().

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

protected

O(1) total energy report. Protected read access for derived classes.

Definition at line 1340 of file LinearMemoryInteractionGraph.cc.

References total_energy_current_state_assignment_.

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

virtual

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

Definition at line 1381 of file LinearMemoryInteractionGraph.cc.

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

LinearMemNode const* core::pack::interaction_graph::LinearMemoryInteractionGraph::get_linmem_node ( int index) const

inlineprotected

Definition at line 413 of file LinearMemoryInteractionGraph.hh.

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

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

LinearMemNode* core::pack::interaction_graph::LinearMemoryInteractionGraph::get_linmem_node ( int index)

inlineprotected

Definition at line 419 of file LinearMemoryInteractionGraph.hh.

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

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

private

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

virtual

iterate across edges and nodes and allow them to prepare for simulated annealing

Edges may decide to delete themselves during this subroutine; therefore edges are prepared first. Afterwards, the nodes must update their edge vector representation.

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

Definition at line 1405 of file LinearMemoryInteractionGraph.cc.

References first_time_prepping_for_simA_, core::pack::interaction_graph::InteractionGraphBase::prepare_for_simulated_annealing(), and set_recent_history_sizes().

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

virtual

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

Definition at line 1358 of file LinearMemoryInteractionGraph.cc.

References core::pack::interaction_graph::LinearMemNode::get_current_state(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), get_linmem_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::T(), and total_energy_current_state_assignment_.

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

virtual

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

Definition at line 1377 of file LinearMemoryInteractionGraph.cc.

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

virtual

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

Definition at line 1267 of file LinearMemoryInteractionGraph.cc.

References core::pack::interaction_graph::LinearMemNode::complete_state_assignment(), get_linmem_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), have_not_committed_last_substitution_, core::pack::interaction_graph::LinearMemNode::partial_assign_state(), total_energy_current_state_assignment_, and update_internal_energy_totals().

void core::pack::interaction_graph::LinearMemoryInteractionGraph::set_recent_history_sizes ( )

private

Definition at line 1471 of file LinearMemoryInteractionGraph.cc.

References get_linmem_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), and core::pack::interaction_graph::LinearMemNode::set_recent_history_size().

Referenced by prepare_for_simulated_annealing().

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

virtual

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

Definition at line 1257 of file LinearMemoryInteractionGraph.cc.

References core::pack::interaction_graph::LinearMemNode::assign_state(), get_linmem_node(), have_not_committed_last_substitution_, total_energy_current_state_assignment_, and update_internal_energy_totals().

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

protected

Definition at line 1451 of file LinearMemoryInteractionGraph.cc.

References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), get_linmem_node(), 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

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

staticprivate

Definition at line 436 of file LinearMemoryInteractionGraph.hh.

Referenced by commit_considered_substitution().

bool core::pack::interaction_graph::LinearMemoryInteractionGraph::first_time_prepping_for_simA_

private

Definition at line 428 of file LinearMemoryInteractionGraph.hh.

Referenced by prepare_for_simulated_annealing().

bool core::pack::interaction_graph::LinearMemoryInteractionGraph::have_not_committed_last_substitution_

private

Definition at line 434 of file LinearMemoryInteractionGraph.hh.

Referenced by blanket_assign_state_0(), commit_considered_substitution(), consider_substitution(), set_network_state(), and set_state_for_node().

int core::pack::interaction_graph::LinearMemoryInteractionGraph::node_considering_alt_state_

private

Definition at line 432 of file LinearMemoryInteractionGraph.hh.

Referenced by commit_considered_substitution(), and consider_substitution().

int core::pack::interaction_graph::LinearMemoryInteractionGraph::num_commits_since_last_update_

private

Definition at line 429 of file LinearMemoryInteractionGraph.hh.

Referenced by commit_considered_substitution(), and update_internal_energy_totals().

core::PackerEnergy core::pack::interaction_graph::LinearMemoryInteractionGraph::total_energy_alternate_state_assignment_

private

Definition at line 431 of file LinearMemoryInteractionGraph.hh.

Referenced by commit_considered_substitution(), and consider_substitution().

core::PackerEnergy core::pack::interaction_graph::LinearMemoryInteractionGraph::total_energy_current_state_assignment_

private

Definition at line 430 of file LinearMemoryInteractionGraph.hh.

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

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation