#include <SymmLinMemInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SymmLinearMemNode:

Collaboration diagram for core::pack::interaction_graph::SymmLinearMemNode:

Public Member Functions
	SymmLinearMemNode (InteractionGraphBase *owner, int node_id, int num_states)
	main constructor, no default ctor, uncopyable More...

virtual	~SymmLinearMemNode ()
	virtual dstor More...

virtual void	prepare_for_simulated_annealing ()
	symmlinmem ig does not have to do anything before sim annealing begins More...

virtual void	print () const
	write internal energy and bookkeeping data to standard out More...

virtual bool	state_unassigned () const
	state 0 represents the unasigned state More...

virtual core::PackerEnergy	get_totalE () const
	return the total energy for this node; includes full energies to neighboring residues More...

void	assign_zero_state ()
	set to state 0 More...

void	assign_state (int new_state)
	set to a particular state – updates the energies internally More...

void	partial_assign_state (int new_state)
	first half of an entire-graph state assignment that avoids unnecessary energy updates as produced in assign_state. Adjust all node's states first, then update all energies. More...

void	complete_state_assignment ()
	second half of the entire-graph state assignment. More...

int	get_current_state () const
	return the index of the currently assigned state More...

int	get_curr_state_recent_state_id () const
	return the "recent state id" for the currently assigned state More...

core::PackerEnergy	get_one_body_energy_current_state () const
	return the one-body energy for the currently assigned state More...

core::PackerEnergy	project_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_node_energy)
	compute the change in energy induced by substituting the currently assigned state with some alternative state More...

void	commit_considered_substitution ()
	proceed to change the currently assigned state to the alternative state considered in the last call to project_deltaE_for_substitution More...

void	acknowledge_last_substititon_not_committed ()
	update bookkeeping info to acknolwedge that the last alternative state considered was not in fact chosen for the currently assigned state. More...

core::PackerEnergy	compute_pair_energy_for_current_state (int edge_making_energy_request)
	comupute the interaction energy between the currently assigned state on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two More...

core::PackerEnergy	compute_pair_energy_for_alternate_state (int edge_making_energy_request)
	comupute the interaction energy between the alternate state being considered on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two More...

void	acknowledge_neighbors_state_substitution (int edge_to_altered_neighbor, core::PackerEnergy new_edge_energy, int other_node_new_state, int other_node_recent_history_index)

void	acknowledge_neighbors_partial_state_substitution (int edge_to_altered_neighbor, int other_node_new_state, int other_state_recent_history_index)

void	set_recent_history_size (int num_states_to_maintain_in_recent_history)

int	get_recent_history_size () const

void	print_internal_energies () const

void	update_internal_energy_sums ()

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

SymmLinearMemEdge const *	get_incident_symmlinmem_edge (int index) const

SymmLinearMemEdge *	get_incident_symmlinmem_edge (int index)

SymmLinearMemNode const *	get_adjacent_symmlinmem_node (int index) const

SymmLinearMemNode *	get_adjacent_symmlinmem_node (int index)

SymmLinearMemoryInteractionGraph const *	get_symmlinmem_ig_owner () const

SymmLinearMemoryInteractionGraph *	get_symmlinmem_ig_owner ()

Public Member Functions inherited from core::pack::interaction_graph::SymmOnTheFlyNode
	SymmOnTheFlyNode (InteractionGraphBase *owner, int node_id, int num_states)
	main constructor, no default or copy constructors More...

virtual	~SymmOnTheFlyNode ()

void	set_rotamers (rotamer_set::RotamerSetCOP rotamers)

virtual void	zero_one_body_energies ()

virtual void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b)

virtual void	update_one_body_energy (int state, core::PackerEnergy energy)

virtual void	set_one_body_energy (int state, core::PackerEnergy energy)

virtual void	add_to_one_body_energy (int state, core::PackerEnergy energy)

virtual void	zero_one_body_energy (int state)

int	get_num_res_types () const
	the number of distinct ResidueType objects pointed to by all of the rotamrs for this node. More...

int	get_num_restype_groups () const
	the number of ResidueType groups, as defined by the RotamerSet's logic for grouping different ResidueType objects which have the same "name3" and the same neighbor radius. More...

utility::vector1< int > &	get_num_states_for_restype_group ()

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

int	get_num_states_for_restype_group (int restype_group)

int	get_state_offset_for_restype_group (int restype_group) const

core::PackerEnergy	get_one_body_energy (int state) const

bool	distinguish_backbone_and_sidechain () const

void	distinguish_backbone_and_sidechain (bool setting)

core::PackerEnergy	compute_rotamer_pair_energy (int edge_making_energy_request, int state_this, int state_other) const

conformation::Residue const &	get_rotamer (int state, int subunit) const
	Returns a reference to the rotamer object in the requested subunit. This reference is valid only until the next call to get_rotamer, and which point, the coordinates inside the requested rotamer may change. More...

BoundingSphere	sc_bounding_sphere (int state, int subunit) const
	Returns a bounding sphere for the sidechain of a given state on a particular subunit. More...

BoundingSphere	bb_bounding_sphere (int subunit) const
	Returns a bounding sphere for the backbone on a particular subunit. More...

SymmOnTheFlyEdge *	get_incident_otf_edge (int edge)

SymmOnTheFlyEdge const *	get_incident_otf_edge (int edge) const

SymmOnTheFlyNode *	get_adjacent_otf_node (int index)

SymmOnTheFlyNode const *	get_adjacent_otf_node (int index) const

SymmOnTheFlyInteractionGraph *	get_on_the_fly_owner ()

SymmOnTheFlyInteractionGraph const *	get_on_the_fly_owner () const

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

	FixedBBNode (InteractionGraphBase *owner, int node_id, int num_states)

Public Member Functions inherited from core::pack::interaction_graph::NodeBase
virtual	~NodeBase ()
	virtual destructor More...

	NodeBase (InteractionGraphBase *, int node_id, int num_states)
	Main constructor, no default constructor nor copy constructor. More...

int	get_num_states () const
	returns the number of states for this node More...

std::list< EdgeBase * >::iterator	add_edge (EdgeBase *edge_ptr)
	adds edge pointer to edge list; returns an iterator to the new list element More...

void	drop_edge (std::list< EdgeBase * >::iterator edge_iterator)
	removes an edge iterator from the node's edge list More...

void	drop_all_edges ()
	deletes all edges incident upon this node More...

EdgeBase *	find_edge (int other_node_index) const
	a slow (linear) search for an edge. The edge is identified by the index of the node to which the edge connects this node. Returns NULL when there is no such connecting edge. More...

void	depth_first_connected_component_counting ()
	performs a depth first traversal of the graph. Each node informs the graph that the traversal resulted in arriving at the node. More...

std::list< EdgeBase * > ::const_iterator	edge_list_begin ()

std::list< EdgeBase * > ::const_iterator	edge_list_end ()

int	get_node_index () const

int	get_num_incident_edges () const

int	get_num_edges_to_smaller_indexed_nodes () const

int	get_num_edges_to_larger_indexed_nodes () const

EdgeBase const *	get_incident_edge (int index) const
	These functions are public for the sake of writing good unit tests. More...

EdgeBase *	get_incident_edge (int index)

int	get_index_of_adjacent_node (int index) const

NodeBase const *	get_adjacent_node (int index) const

NodeBase *	get_adjacent_node (int index)

Private Member Functions
void	update_internal_vectors ()

int	update_recent_history (int state)

Private Attributes
utility::recent_history_queue	rhq_
	Data. More...

utility::vector1< int >	neighbors_curr_state_

utility::vector1< int >	neighbors_state_recent_history_index_

int	current_state_

core::PackerEnergy	curr_state_one_body_energy_

core::PackerEnergy	curr_state_total_energy_

utility::vector1 < core::PackerEnergy >	curr_state_two_body_energies_

int	alternate_state_

core::PackerEnergy	alternate_state_one_body_energy_

core::PackerEnergy	alternate_state_total_energy_

utility::vector1 < core::PackerEnergy >	alternate_state_two_body_energies_

bool	alternate_state_is_being_considered_

bool	already_prepped_for_simA_

ObjexxFCL::FArray1D_int	accepted_rejected_substitution_history_

int	accepted_history_head_

int	num_recently_accepted_

bool	filled_substitution_history_

Static Private Attributes
static const int	ACCEPTED = 1

static const int	REJECTED = 0

static const int	ACCEPTANCE_REJECTION_HISTORY_LENGTH = 100

static const int	THRESHOLD_ACCEPTANCE_RATE_FOR_RPE_STORAGE = 10

Additional Inherited Members
Public Types inherited from core::pack::interaction_graph::SymmOnTheFlyNode
typedef std::pair< Vector, Real >	BoundingSphere

Protected Member Functions inherited from core::pack::interaction_graph::NodeBase
void	update_edge_vector ()
	converts edge-list to edge-vector representation More...

bool	get_edge_vector_up_to_date () const

InteractionGraphBase const *	get_owner () const

InteractionGraphBase *	get_owner ()

Detailed Description

Definition at line 33 of file SymmLinMemInteractionGraph.hh.

Constructor & Destructor Documentation

core::pack::interaction_graph::SymmLinearMemNode::SymmLinearMemNode	(	InteractionGraphBase *	owner,
		int	node_id,
		int	num_states
	)

main constructor, no default ctor, uncopyable

main constructor, no default or copy constructors

Definition at line 48 of file SymmLinMemInteractionGraph.cc.

References rhq_.

Referenced by count_static_memory().

core::pack::interaction_graph::SymmLinearMemNode::~SymmLinearMemNode ( )

virtual

virtual dstor

Definition at line 70 of file SymmLinMemInteractionGraph.cc.

Member Function Documentation

void core::pack::interaction_graph::SymmLinearMemNode::acknowledge_last_substititon_not_committed ( )

update bookkeeping info to acknolwedge that the last alternative state considered was not in fact chosen for the currently assigned state.

Definition at line 605 of file SymmLinMemInteractionGraph.cc.

References ACCEPTANCE_REJECTION_HISTORY_LENGTH, ACCEPTED, accepted_history_head_, accepted_rejected_substitution_history_, alternate_state_is_being_considered_, filled_substitution_history_, num_recently_accepted_, and REJECTED.

void core::pack::interaction_graph::SymmLinearMemNode::acknowledge_neighbors_partial_state_substitution	(	int	edge_to_altered_neighbor,
		int	other_node_new_state,
		int	other_state_recent_history_index
	)

Definition at line 644 of file SymmLinMemInteractionGraph.cc.

References curr_state_total_energy_, curr_state_two_body_energies_, neighbors_curr_state_, and neighbors_state_recent_history_index_.

void core::pack::interaction_graph::SymmLinearMemNode::acknowledge_neighbors_state_substitution	(	int	edge_to_altered_neighbor,
		core::PackerEnergy	new_edge_energy,
		int	other_node_new_state,
		int	other_node_recent_history_index
	)

inline

Definition at line 485 of file SymmLinMemInteractionGraph.hh.

References curr_state_total_energy_, curr_state_two_body_energies_, neighbors_curr_state_, and neighbors_state_recent_history_index_.

void core::pack::interaction_graph::SymmLinearMemNode::assign_state ( int new_state)

set to a particular state – updates the energies internally

Definition at line 177 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_state_change(), alternate_state_is_being_considered_, assign_zero_state(), curr_state_one_body_energy_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, core::pack::interaction_graph::debug, get_incident_symmlinmem_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::NodeBase::get_num_states(), core::pack::interaction_graph::SymmOnTheFlyNode::get_one_body_energy(), rhq_, and update_recent_history().

Referenced by core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::set_state_for_node().

void core::pack::interaction_graph::SymmLinearMemNode::assign_zero_state ( )

virtual

set to state 0

puts the symmlinmemNode in the unassigned state

Implements core::pack::interaction_graph::NodeBase.

Definition at line 152 of file SymmLinMemInteractionGraph.cc.

References alternate_state_, alternate_state_is_being_considered_, curr_state_one_body_energy_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, get_incident_symmlinmem_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

Referenced by assign_state(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::blanket_assign_state_0(), and partial_assign_state().

void core::pack::interaction_graph::SymmLinearMemNode::commit_considered_substitution ( )

proceed to change the currently assigned state to the alternative state considered in the last call to project_deltaE_for_substitution

commits the last substitution that was considered by this Node

Definition at line 554 of file SymmLinMemInteractionGraph.cc.

References ACCEPTANCE_REJECTION_HISTORY_LENGTH, ACCEPTED, accepted_history_head_, accepted_rejected_substitution_history_, core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_substitution(), alternate_state_, alternate_state_is_being_considered_, alternate_state_one_body_energy_, alternate_state_total_energy_, alternate_state_two_body_energies_, curr_state_one_body_energy_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, core::pack::interaction_graph::debug, filled_substitution_history_, get_incident_symmlinmem_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), neighbors_curr_state_, num_recently_accepted_, REJECTED, rhq_, and update_recent_history().

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

void core::pack::interaction_graph::SymmLinearMemNode::complete_state_assignment ( )

second half of the entire-graph state assignment.

Definition at line 238 of file SymmLinMemInteractionGraph.cc.

References curr_state_one_body_energy_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, get_incident_symmlinmem_edge(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and core::pack::interaction_graph::SymmOnTheFlyNode::get_one_body_energy().

Referenced by core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::set_network_state().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::compute_pair_energy_for_alternate_state ( int edge_making_energy_request)

comupute the interaction energy between the alternate state being considered on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

Definition at line 632 of file SymmLinMemInteractionGraph.cc.

References alternate_state_, core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), and neighbors_curr_state_.

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::compute_pair_energy_for_current_state ( int edge_making_energy_request)

comupute the interaction energy between the currently assigned state on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

Definition at line 621 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), current_state_, and neighbors_curr_state_.

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

virtual

reports the amount of dynamic memory this node allocates recursing to its base class

Reimplemented from core::pack::interaction_graph::SymmOnTheFlyNode.

Definition at line 135 of file SymmLinMemInteractionGraph.cc.

References alternate_state_two_body_energies_, core::pack::interaction_graph::SymmOnTheFlyNode::count_dynamic_memory(), curr_state_two_body_energies_, neighbors_curr_state_, neighbors_state_recent_history_index_, and rhq_.

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

virtual

Implements core::pack::interaction_graph::SymmOnTheFlyNode.

Definition at line 129 of file SymmLinMemInteractionGraph.cc.

References SymmLinearMemNode().

SymmLinearMemNode const * core::pack::interaction_graph::SymmLinearMemNode::get_adjacent_symmlinmem_node ( int index) const

inline

Definition at line 403 of file SymmLinMemInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_adjacent_node().

SymmLinearMemNode * core::pack::interaction_graph::SymmLinearMemNode::get_adjacent_symmlinmem_node ( int index)

inline

Definition at line 410 of file SymmLinMemInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_adjacent_node().

int core::pack::interaction_graph::SymmLinearMemNode::get_curr_state_recent_state_id ( ) const

inline

return the "recent state id" for the currently assigned state

Definition at line 74 of file SymmLinMemInteractionGraph.hh.

References rhq_.

Referenced by core::pack::interaction_graph::SymmLinearMemEdge::store_curr_state_energy().

int core::pack::interaction_graph::SymmLinearMemNode::get_current_state ( ) const

inline

return the index of the currently assigned state

Definition at line 68 of file SymmLinMemInteractionGraph.hh.

References current_state_.

Referenced by core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::print_current_state_assignment(), and core::pack::interaction_graph::SymmLinearMemEdge::store_curr_state_energy().

SymmLinearMemEdge const * core::pack::interaction_graph::SymmLinearMemNode::get_incident_symmlinmem_edge ( int index) const

inline

Definition at line 389 of file SymmLinMemInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_incident_edge().

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), complete_state_assignment(), partial_assign_state(), prepare_for_simulated_annealing(), and update_internal_energy_sums().

SymmLinearMemEdge * core::pack::interaction_graph::SymmLinearMemNode::get_incident_symmlinmem_edge ( int index)

inline

Definition at line 396 of file SymmLinMemInteractionGraph.hh.

References core::pack::interaction_graph::NodeBase::get_incident_edge().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::get_one_body_energy_current_state ( ) const

inline

return the one-body energy for the currently assigned state

Definition at line 79 of file SymmLinMemInteractionGraph.hh.

References curr_state_one_body_energy_.

Referenced by core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::get_energy_sum_for_vertex_group().

int core::pack::interaction_graph::SymmLinearMemNode::get_recent_history_size ( ) const

Definition at line 667 of file SymmLinMemInteractionGraph.cc.

References rhq_.

SymmLinearMemoryInteractionGraph const * core::pack::interaction_graph::SymmLinearMemNode::get_symmlinmem_ig_owner ( ) const

inline

Definition at line 375 of file SymmLinMemInteractionGraph.hh.

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

SymmLinearMemoryInteractionGraph * core::pack::interaction_graph::SymmLinearMemNode::get_symmlinmem_ig_owner ( )

inline

Definition at line 382 of file SymmLinMemInteractionGraph.hh.

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

virtual core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::get_totalE ( ) const

inlinevirtual

return the total energy for this node; includes full energies to neighboring residues

Definition at line 54 of file SymmLinMemInteractionGraph.hh.

References curr_state_total_energy_.

void core::pack::interaction_graph::SymmLinearMemNode::partial_assign_state ( int new_state)

first half of an entire-graph state assignment that avoids unnecessary energy updates as produced in assign_state. Adjust all node's states first, then update all energies.

Definition at line 214 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_partial_state_change(), alternate_state_is_being_considered_, assign_zero_state(), current_state_, get_incident_symmlinmem_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), rhq_, and update_recent_history().

Referenced by core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::set_network_state().

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

virtual

symmlinmem ig does not have to do anything before sim annealing begins

Implements core::pack::interaction_graph::NodeBase.

Definition at line 74 of file SymmLinMemInteractionGraph.cc.

References accepted_history_head_, already_prepped_for_simA_, filled_substitution_history_, core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date(), get_incident_symmlinmem_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::NodeBase::get_num_states(), num_recently_accepted_, core::pack::interaction_graph::SymmLinearMemEdge::reset_state_energies(), rhq_, and update_internal_vectors().

void core::pack::interaction_graph::SymmLinearMemNode::print ( ) const

virtual

write internal energy and bookkeeping data to standard out

Implements core::pack::interaction_graph::NodeBase.

Definition at line 103 of file SymmLinMemInteractionGraph.cc.

References alternate_state_is_being_considered_, alternate_state_one_body_energy_, alternate_state_two_body_energies_, curr_state_one_body_energy_, curr_state_two_body_energies_, current_state_, core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::NodeBase::get_num_states(), and core::pack::interaction_graph::T().

Referenced by core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::print_current_state_assignment().

void core::pack::interaction_graph::SymmLinearMemNode::print_internal_energies ( ) const

Definition at line 674 of file SymmLinMemInteractionGraph.cc.

References curr_state_one_body_energy_, curr_state_total_energy_, curr_state_two_body_energies_, current_state_, core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and core::pack::interaction_graph::T().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::project_deltaE_for_substitution	(	int	alternate_state,
		core::PackerEnergy &	prev_node_energy
	)

compute the change in energy induced by substituting the currently assigned state with some alternative state

Definition at line 254 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::debug.

void core::pack::interaction_graph::SymmLinearMemNode::set_recent_history_size ( int num_states_to_maintain_in_recent_history)

Definition at line 659 of file SymmLinMemInteractionGraph.cc.

References rhq_.

Referenced by core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::set_recent_history_sizes().

virtual bool core::pack::interaction_graph::SymmLinearMemNode::state_unassigned ( ) const

inlinevirtual

state 0 represents the unasigned state

Implements core::pack::interaction_graph::NodeBase.

Definition at line 52 of file SymmLinMemInteractionGraph.hh.

References current_state_.

void core::pack::interaction_graph::SymmLinearMemNode::update_internal_energy_sums ( )

Definition at line 689 of file SymmLinMemInteractionGraph.cc.

References curr_state_one_body_energy_, curr_state_total_energy_, core::pack::interaction_graph::SymmLinearMemEdge::get_current_two_body_energy(), core::pack::interaction_graph::NodeBase::get_edge_vector_up_to_date(), get_incident_symmlinmem_edge(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

void core::pack::interaction_graph::SymmLinearMemNode::update_internal_vectors ( )

private

Definition at line 703 of file SymmLinMemInteractionGraph.cc.

References alternate_state_two_body_energies_, curr_state_two_body_energies_, core::pack::interaction_graph::NodeBase::get_num_incident_edges(), neighbors_curr_state_, neighbors_state_recent_history_index_, and core::pack::interaction_graph::NodeBase::update_edge_vector().

Referenced by prepare_for_simulated_annealing().

int core::pack::interaction_graph::SymmLinearMemNode::update_recent_history ( int state)

private

Definition at line 719 of file SymmLinMemInteractionGraph.cc.

References rhq_.

Referenced by assign_state(), commit_considered_substitution(), and partial_assign_state().

Member Data Documentation

const int core::pack::interaction_graph::SymmLinearMemNode::ACCEPTANCE_REJECTION_HISTORY_LENGTH = 100

staticprivate

Definition at line 189 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), and commit_considered_substitution().

const int core::pack::interaction_graph::SymmLinearMemNode::ACCEPTED = 1

staticprivate

Definition at line 186 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), and commit_considered_substitution().

int core::pack::interaction_graph::SymmLinearMemNode::accepted_history_head_

private

Definition at line 182 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), commit_considered_substitution(), and prepare_for_simulated_annealing().

ObjexxFCL::FArray1D_int core::pack::interaction_graph::SymmLinearMemNode::accepted_rejected_substitution_history_

private

Definition at line 181 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), and commit_considered_substitution().

bool core::pack::interaction_graph::SymmLinearMemNode::already_prepped_for_simA_

private

Definition at line 179 of file SymmLinMemInteractionGraph.hh.

Referenced by prepare_for_simulated_annealing().

int core::pack::interaction_graph::SymmLinearMemNode::alternate_state_

private

Definition at line 173 of file SymmLinMemInteractionGraph.hh.

Referenced by assign_zero_state(), commit_considered_substitution(), and compute_pair_energy_for_alternate_state().

bool core::pack::interaction_graph::SymmLinearMemNode::alternate_state_is_being_considered_

private

Definition at line 178 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), assign_state(), assign_zero_state(), commit_considered_substitution(), partial_assign_state(), and print().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::alternate_state_one_body_energy_

private

Definition at line 174 of file SymmLinMemInteractionGraph.hh.

Referenced by commit_considered_substitution(), and print().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::alternate_state_total_energy_

private

Definition at line 175 of file SymmLinMemInteractionGraph.hh.

Referenced by commit_considered_substitution().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmLinearMemNode::alternate_state_two_body_energies_

private

Definition at line 176 of file SymmLinMemInteractionGraph.hh.

Referenced by commit_considered_substitution(), count_dynamic_memory(), print(), and update_internal_vectors().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::curr_state_one_body_energy_

private

Definition at line 169 of file SymmLinMemInteractionGraph.hh.

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), complete_state_assignment(), get_one_body_energy_current_state(), print(), print_internal_energies(), and update_internal_energy_sums().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemNode::curr_state_total_energy_

private

Definition at line 170 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_neighbors_partial_state_substitution(), acknowledge_neighbors_state_substitution(), assign_state(), assign_zero_state(), commit_considered_substitution(), complete_state_assignment(), get_totalE(), print_internal_energies(), and update_internal_energy_sums().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmLinearMemNode::curr_state_two_body_energies_

private

Definition at line 171 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_neighbors_partial_state_substitution(), acknowledge_neighbors_state_substitution(), assign_state(), assign_zero_state(), commit_considered_substitution(), complete_state_assignment(), count_dynamic_memory(), print(), print_internal_energies(), and update_internal_vectors().

int core::pack::interaction_graph::SymmLinearMemNode::current_state_

private

Definition at line 168 of file SymmLinMemInteractionGraph.hh.

Referenced by assign_state(), assign_zero_state(), commit_considered_substitution(), complete_state_assignment(), compute_pair_energy_for_current_state(), get_current_state(), partial_assign_state(), print(), print_internal_energies(), and state_unassigned().

bool core::pack::interaction_graph::SymmLinearMemNode::filled_substitution_history_

private

Definition at line 184 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), commit_considered_substitution(), and prepare_for_simulated_annealing().

utility::vector1< int > core::pack::interaction_graph::SymmLinearMemNode::neighbors_curr_state_

private

Definition at line 165 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_neighbors_partial_state_substitution(), acknowledge_neighbors_state_substitution(), commit_considered_substitution(), compute_pair_energy_for_alternate_state(), compute_pair_energy_for_current_state(), count_dynamic_memory(), and update_internal_vectors().

utility::vector1< int > core::pack::interaction_graph::SymmLinearMemNode::neighbors_state_recent_history_index_

private

Definition at line 166 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_neighbors_partial_state_substitution(), acknowledge_neighbors_state_substitution(), count_dynamic_memory(), and update_internal_vectors().

int core::pack::interaction_graph::SymmLinearMemNode::num_recently_accepted_

private

Definition at line 183 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), commit_considered_substitution(), and prepare_for_simulated_annealing().

const int core::pack::interaction_graph::SymmLinearMemNode::REJECTED = 0

staticprivate

Definition at line 187 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), and commit_considered_substitution().

utility::recent_history_queue core::pack::interaction_graph::SymmLinearMemNode::rhq_

private

Data.

Definition at line 163 of file SymmLinMemInteractionGraph.hh.

Referenced by assign_state(), commit_considered_substitution(), count_dynamic_memory(), get_curr_state_recent_state_id(), get_recent_history_size(), partial_assign_state(), prepare_for_simulated_annealing(), set_recent_history_size(), SymmLinearMemNode(), and update_recent_history().

const int core::pack::interaction_graph::SymmLinearMemNode::THRESHOLD_ACCEPTANCE_RATE_FOR_RPE_STORAGE = 10

staticprivate

Definition at line 190 of file SymmLinMemInteractionGraph.hh.

The documentation for this class was generated from the following files:

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

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