#include <LinearMemoryInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::LinearMemNode:

Collaboration diagram for core::pack::interaction_graph::LinearMemNode:

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

virtual	~LinearMemNode ()
	virtual dstor More...

virtual void	prepare_for_simulated_annealing ()
	linmem 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, SparseMatrixIndex const &other_node_new_state_sparse_info, int other_node_recent_history_index)

void	acknowledge_neighbors_partial_state_substitution (int edge_to_altered_neighbor, int other_node_new_state, SparseMatrixIndex const &other_node_new_state_sparse_info, int other_state_recent_history_index)

SparseMatrixIndex const &	get_sparse_mat_info_for_curr_state () const

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

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

virtual	~OnTheFlyNode ()

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_aa_types () const

utility::vector1< int > &	get_num_states_for_aa_types ()

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

int	get_num_states_for_aa_type (int aa_type)

SparseMatrixIndex const &	get_sparse_mat_info_for_state (int state) const

int	get_state_offset_for_aatype (int aatype) 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

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)

Protected Member Functions
conformation::Residue const &	get_current_rotamer ()

core::PackerEnergy	get_curr_pd_energy_total () const

core::PackerEnergy	get_alt_pd_energy_total () const

void	set_alternate_state (int alt)

int	get_alternate_state () const

void	calc_deltaEpd (int alternate_state)

bool	considering_alternate_state () const

Protected Member Functions inherited from core::pack::interaction_graph::OnTheFlyNode
OnTheFlyEdge *	get_incident_otf_edge (int edge)

OnTheFlyEdge const *	get_incident_otf_edge (int edge) const

OnTheFlyNode *	get_adjacent_otf_node (int index)

OnTheFlyNode const *	get_adjacent_otf_node (int index) const

OnTheFlyInteractionGraph *	get_on_the_fly_owner ()

OnTheFlyInteractionGraph const *	get_on_the_fly_owner () const

conformation::Residue const &	get_rotamer (int state) const

BoundingSphere const &	sc_bounding_sphere (int state) const

BoundingSphere const &	bb_bounding_sphere () const

Private Member Functions
void	update_internal_vectors ()

LinearMemEdge const *	get_incident_linmem_edge (int index) const

LinearMemEdge *	get_incident_linmem_edge (int index)

LinearMemNode const *	get_adjacent_linmem_node (int index) const

LinearMemNode *	get_adjacent_linmem_node (int index)

LinearMemoryInteractionGraph const *	get_linmem_ig_owner () const

LinearMemoryInteractionGraph *	get_linmem_ig_owner ()

int	update_recent_history (int state)

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

ObjexxFCL::FArray3D< unsigned char >	aa_neighbors_for_edges_

utility::vector1< int >	neighbors_curr_state_

utility::vector1< int >	neighbors_state_recent_history_index_

utility::vector1 < SparseMatrixIndex >	neighbors_curr_state_sparse_info_

int	current_state_

SparseMatrixIndex	curr_state_sparse_mat_info_

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_

SparseMatrixIndex	alt_state_sparse_mat_info_

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::OnTheFlyNode
typedef std::pair< Vector, Real >	BoundingSphere

Detailed Description

Definition at line 42 of file LinearMemoryInteractionGraph.hh.

Constructor & Destructor Documentation

core::pack::interaction_graph::LinearMemNode::LinearMemNode	(	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 LinearMemoryInteractionGraph.cc.

References rhq_.

Referenced by count_static_memory().

core::pack::interaction_graph::LinearMemNode::~LinearMemNode ( )

virtual

virtual dstor

Definition at line 70 of file LinearMemoryInteractionGraph.cc.

Member Function Documentation

void core::pack::interaction_graph::LinearMemNode::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 634 of file LinearMemoryInteractionGraph.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::LinearMemNode::acknowledge_neighbors_partial_state_substitution	(	int	edge_to_altered_neighbor,
		int	other_node_new_state,
		SparseMatrixIndex const &	other_node_new_state_sparse_info,
		int	other_state_recent_history_index
	)

Definition at line 684 of file LinearMemoryInteractionGraph.cc.

References curr_state_total_energy_, curr_state_two_body_energies_, neighbors_curr_state_, neighbors_curr_state_sparse_info_, and neighbors_state_recent_history_index_.

void core::pack::interaction_graph::LinearMemNode::acknowledge_neighbors_state_substitution	(	int	edge_to_altered_neighbor,
		core::PackerEnergy	new_edge_energy,
		int	other_node_new_state,
		SparseMatrixIndex const &	other_node_new_state_sparse_info,
		int	other_node_recent_history_index
	)

inline

Definition at line 566 of file LinearMemoryInteractionGraph.hh.

References curr_state_total_energy_, curr_state_two_body_energies_, neighbors_curr_state_, neighbors_curr_state_sparse_info_, and neighbors_state_recent_history_index_.

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

set to a particular state – updates the energies internally

Definition at line 182 of file LinearMemoryInteractionGraph.cc.

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

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

virtual

set to state 0

puts the LinMemNode in the unassigned state

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

Definition at line 157 of file LinearMemoryInteractionGraph.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_linmem_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::LinearMemoryInteractionGraph::blanket_assign_state_0(), and partial_assign_state().

void core::pack::interaction_graph::LinearMemNode::calc_deltaEpd ( int alternate_state)

protected

Definition at line 794 of file LinearMemoryInteractionGraph.cc.

References project_deltaE_for_substitution().

void core::pack::interaction_graph::LinearMemNode::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 578 of file LinearMemoryInteractionGraph.cc.

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

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

second half of the entire-graph state assignment.

Definition at line 249 of file LinearMemoryInteractionGraph.cc.

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

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

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::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 672 of file LinearMemoryInteractionGraph.cc.

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

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::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 652 of file LinearMemoryInteractionGraph.cc.

References aa_neighbors_for_edges_, core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), curr_state_sparse_mat_info_, current_state_, core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), neighbors_curr_state_, and neighbors_curr_state_sparse_info_.

bool core::pack::interaction_graph::LinearMemNode::considering_alternate_state ( ) const

inlineprotected

Definition at line 164 of file LinearMemoryInteractionGraph.hh.

References alternate_state_is_being_considered_.

unsigned int core::pack::interaction_graph::LinearMemNode::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::OnTheFlyNode.

Definition at line 138 of file LinearMemoryInteractionGraph.cc.

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

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

virtual

Implements core::pack::interaction_graph::OnTheFlyNode.

Definition at line 132 of file LinearMemoryInteractionGraph.cc.

References LinearMemNode().

LinearMemNode const * core::pack::interaction_graph::LinearMemNode::get_adjacent_linmem_node ( int index) const

inlineprivate

Definition at line 475 of file LinearMemoryInteractionGraph.hh.

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

LinearMemNode * core::pack::interaction_graph::LinearMemNode::get_adjacent_linmem_node ( int index)

inlineprivate

Definition at line 482 of file LinearMemoryInteractionGraph.hh.

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

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::get_alt_pd_energy_total ( ) const

inlineprotected

Definition at line 159 of file LinearMemoryInteractionGraph.hh.

References alternate_state_total_energy_.

int core::pack::interaction_graph::LinearMemNode::get_alternate_state ( ) const

inlineprotected

Definition at line 161 of file LinearMemoryInteractionGraph.hh.

References alternate_state_.

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::get_curr_pd_energy_total ( ) const

inlineprotected

Definition at line 158 of file LinearMemoryInteractionGraph.hh.

References curr_state_total_energy_.

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

inline

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

Definition at line 83 of file LinearMemoryInteractionGraph.hh.

References rhq_.

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

conformation::Residue const& core::pack::interaction_graph::LinearMemNode::get_current_rotamer ( )

inlineprotected

Definition at line 151 of file LinearMemoryInteractionGraph.hh.

References current_state_, and core::pack::interaction_graph::OnTheFlyNode::get_rotamer().

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

inline

return the index of the currently assigned state

Definition at line 77 of file LinearMemoryInteractionGraph.hh.

References current_state_.

Referenced by core::pack::interaction_graph::LinearMemoryInteractionGraph::print_current_state_assignment(), and core::pack::interaction_graph::LinearMemEdge::store_curr_state_energy().

LinearMemEdge const * core::pack::interaction_graph::LinearMemNode::get_incident_linmem_edge ( int index) const

inlineprivate

Definition at line 461 of file LinearMemoryInteractionGraph.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(), update_internal_energy_sums(), and update_internal_vectors().

LinearMemEdge * core::pack::interaction_graph::LinearMemNode::get_incident_linmem_edge ( int index)

inlineprivate

Definition at line 468 of file LinearMemoryInteractionGraph.hh.

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

LinearMemoryInteractionGraph const * core::pack::interaction_graph::LinearMemNode::get_linmem_ig_owner ( ) const

inlineprivate

Definition at line 447 of file LinearMemoryInteractionGraph.hh.

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

LinearMemoryInteractionGraph * core::pack::interaction_graph::LinearMemNode::get_linmem_ig_owner ( )

inlineprivate

Definition at line 454 of file LinearMemoryInteractionGraph.hh.

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

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

inline

return the one-body energy for the currently assigned state

Definition at line 88 of file LinearMemoryInteractionGraph.hh.

References curr_state_one_body_energy_.

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

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

Definition at line 710 of file LinearMemoryInteractionGraph.cc.

References rhq_.

SparseMatrixIndex const & core::pack::interaction_graph::LinearMemNode::get_sparse_mat_info_for_curr_state ( ) const

inline

Definition at line 519 of file LinearMemoryInteractionGraph.hh.

References current_state_, and core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state().

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

inlinevirtual

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

Definition at line 63 of file LinearMemoryInteractionGraph.hh.

References curr_state_total_energy_.

void core::pack::interaction_graph::LinearMemNode::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 222 of file LinearMemoryInteractionGraph.cc.

References core::pack::interaction_graph::LinearMemEdge::acknowledge_partial_state_change(), alternate_state_is_being_considered_, assign_zero_state(), curr_state_sparse_mat_info_, current_state_, get_incident_linmem_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state(), rhq_, and update_recent_history().

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

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

virtual

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

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

Definition at line 74 of file LinearMemoryInteractionGraph.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_linmem_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::LinearMemEdge::reset_state_energies(), rhq_, and update_internal_vectors().

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

virtual

write internal energy and bookkeeping data to standard out

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

Definition at line 103 of file LinearMemoryInteractionGraph.cc.

References alternate_state_is_being_considered_, alternate_state_one_body_energy_, alternate_state_two_body_energies_, curr_state_one_body_energy_, curr_state_sparse_mat_info_, curr_state_two_body_energies_, current_state_, core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), 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(), core::pack::interaction_graph::SparseMatrixIndex::get_state_ind_for_this_aa_type(), and core::pack::interaction_graph::T().

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

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

Definition at line 717 of file LinearMemoryInteractionGraph.cc.

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

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::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 267 of file LinearMemoryInteractionGraph.cc.

References core::graph::Node::const_edge_list_begin(), core::graph::Node::const_edge_list_end(), core::pack::interaction_graph::debug, protocols::comparative_modeling::features::E, core::scoring::fa_rep, core::graph::Graph::get_node(), core::scoring::EMapVector::show_nonzero(), core::pack::interaction_graph::T(), and core::scoring::EMapVector::zero().

Referenced by calc_deltaEpd().

void core::pack::interaction_graph::LinearMemNode::set_alternate_state ( int alt)

inlineprotected

Definition at line 160 of file LinearMemoryInteractionGraph.hh.

References alternate_state_.

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

Definition at line 702 of file LinearMemoryInteractionGraph.cc.

References rhq_.

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

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

inlinevirtual

state 0 represents the unasigned state

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

Definition at line 61 of file LinearMemoryInteractionGraph.hh.

References current_state_.

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

Definition at line 735 of file LinearMemoryInteractionGraph.cc.

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

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

private

Definition at line 750 of file LinearMemoryInteractionGraph.cc.

References aa_neighbors_for_edges_, alternate_state_two_body_energies_, curr_state_two_body_energies_, get_incident_linmem_edge(), core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::OnTheFlyNode::get_num_aa_types(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), core::pack::interaction_graph::LinearMemEdge::get_sparse_aa_neighbor_info(), neighbors_curr_state_, neighbors_curr_state_sparse_info_, 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::LinearMemNode::update_recent_history ( int state)

private

Definition at line 801 of file LinearMemoryInteractionGraph.cc.

References rhq_.

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

Member Data Documentation

ObjexxFCL::FArray3D< unsigned char > core::pack::interaction_graph::LinearMemNode::aa_neighbors_for_edges_

private

Definition at line 199 of file LinearMemoryInteractionGraph.hh.

Referenced by compute_pair_energy_for_current_state(), count_dynamic_memory(), and update_internal_vectors().

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

staticprivate

Definition at line 227 of file LinearMemoryInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), and commit_considered_substitution().

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

staticprivate

Definition at line 224 of file LinearMemoryInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), and commit_considered_substitution().

int core::pack::interaction_graph::LinearMemNode::accepted_history_head_

private

Definition at line 220 of file LinearMemoryInteractionGraph.hh.

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

ObjexxFCL::FArray1D_int core::pack::interaction_graph::LinearMemNode::accepted_rejected_substitution_history_

private

Definition at line 219 of file LinearMemoryInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), and commit_considered_substitution().

bool core::pack::interaction_graph::LinearMemNode::already_prepped_for_simA_

private

Definition at line 217 of file LinearMemoryInteractionGraph.hh.

Referenced by prepare_for_simulated_annealing().

SparseMatrixIndex core::pack::interaction_graph::LinearMemNode::alt_state_sparse_mat_info_

private

Definition at line 211 of file LinearMemoryInteractionGraph.hh.

Referenced by commit_considered_substitution().

int core::pack::interaction_graph::LinearMemNode::alternate_state_

private

Definition at line 210 of file LinearMemoryInteractionGraph.hh.

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

bool core::pack::interaction_graph::LinearMemNode::alternate_state_is_being_considered_

private

Definition at line 216 of file LinearMemoryInteractionGraph.hh.

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

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::alternate_state_one_body_energy_

private

Definition at line 212 of file LinearMemoryInteractionGraph.hh.

Referenced by commit_considered_substitution(), and print().

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::alternate_state_total_energy_

private

Definition at line 213 of file LinearMemoryInteractionGraph.hh.

Referenced by commit_considered_substitution(), and get_alt_pd_energy_total().

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

private

Definition at line 214 of file LinearMemoryInteractionGraph.hh.

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

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::curr_state_one_body_energy_

private

Definition at line 206 of file LinearMemoryInteractionGraph.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().

SparseMatrixIndex core::pack::interaction_graph::LinearMemNode::curr_state_sparse_mat_info_

private

Definition at line 205 of file LinearMemoryInteractionGraph.hh.

Referenced by assign_state(), commit_considered_substitution(), compute_pair_energy_for_current_state(), partial_assign_state(), print(), and print_internal_energies().

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::curr_state_total_energy_

private

Definition at line 207 of file LinearMemoryInteractionGraph.hh.

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

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

private

Definition at line 208 of file LinearMemoryInteractionGraph.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::LinearMemNode::current_state_

private

Definition at line 204 of file LinearMemoryInteractionGraph.hh.

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

bool core::pack::interaction_graph::LinearMemNode::filled_substitution_history_

private

Definition at line 222 of file LinearMemoryInteractionGraph.hh.

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

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

private

Definition at line 200 of file LinearMemoryInteractionGraph.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< SparseMatrixIndex > core::pack::interaction_graph::LinearMemNode::neighbors_curr_state_sparse_info_

private

Definition at line 202 of file LinearMemoryInteractionGraph.hh.

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

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

private

Definition at line 201 of file LinearMemoryInteractionGraph.hh.

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

int core::pack::interaction_graph::LinearMemNode::num_recently_accepted_

private

Definition at line 221 of file LinearMemoryInteractionGraph.hh.

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

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

staticprivate

Definition at line 225 of file LinearMemoryInteractionGraph.hh.

Referenced by acknowledge_last_substititon_not_committed(), and commit_considered_substitution().

utility::recent_history_queue core::pack::interaction_graph::LinearMemNode::rhq_

private

Data.

Definition at line 197 of file LinearMemoryInteractionGraph.hh.

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

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

staticprivate

Definition at line 228 of file LinearMemoryInteractionGraph.hh.

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

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