#include <SymmLinMemInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SymmLinearMemEdge:

Collaboration diagram for core::pack::interaction_graph::SymmLinearMemEdge:

Public Member Functions
	SymmLinearMemEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)

virtual	~SymmLinearMemEdge ()

virtual core::PackerEnergy	get_two_body_energy (int const node1state, int const node2state) const

virtual void	prepare_for_simulated_annealing ()

core::PackerEnergy	get_current_two_body_energy () const

void	acknowledge_state_change (int node_ind, int new_state, int bumped_recent_history_index, int new_state_recent_history_index, core::PackerEnergy &new_energy)

void	acknowledge_state_zeroed (int node_ind)

void	acknowledge_partial_state_change (int node_ind, int new_state, int bumped_recent_history_index, int new_state_recent_history_index)

core::PackerEnergy	get_energy_following_partial_state_assignment ()

void	reset_state_energies (int node_index, int state, int recent_history_id)

core::PackerEnergy	get_energy_for_alt_state (bool store_rpes, int changing_node_index, int alternate_state, int alternate_state_recent_history_index, int other_node_curr_state, int other_node_state_recent_history_index)

void	acknowledge_substitution (int substituted_node_index, core::PackerEnergy const curr_state_energy, int nodes_new_state, int bumped_recent_history_index, int new_state_recent_history_index, int neighbors_curr_state)

int	get_two_body_table_size () const

virtual void	declare_energies_final ()

void	print_current_energy () const

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

virtual void	set_edge_weight (Real weight)

SymmLinearMemNode const *	get_symmlinmem_node (int index) const

SymmLinearMemNode *	get_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::SymmOnTheFlyEdge
virtual	~SymmOnTheFlyEdge ()

	SymmOnTheFlyEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)

void	add_ProCorrection_values (int node_not_necessarily_proline, int state, core::PackerEnergy bb_nonprobb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_nonprobb_E, core::PackerEnergy sc_probb_E)

core::PackerEnergy	get_proline_correction_for_node (int node_ind, int state) const

bool	long_range_interactions_exist () const

bool	short_range_interactions_exist () const

void	note_long_range_interactions_exist ()

void	note_short_range_interactions_exist ()

ResiduePairEvalType	eval_type (int node_index) const

void	set_residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit)

unsigned char	residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit, int whichnode_restypegroup, int othernode_restypegroup) const

virtual void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &)
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

virtual bool	get_sparse_aa_info (int, int) const
	fullfilling base class virtual member request – however, this function does not quite make sense for a symmetric otf ig, so this is just stubbed out to return true. More...

virtual void	force_aa_neighbors (int, int)
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

virtual void	force_all_aa_neighbors ()
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

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

	FixedBBEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)

Public Member Functions inherited from core::pack::interaction_graph::EdgeBase
virtual	~EdgeBase ()
	copy constructor, do not use More...

	EdgeBase (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
	main constructor for edge, no default nor copy constructors More...

int	get_other_ind (int callers_index) const
	returns the index of the other node that the edge is incident upon More...

NodeBase *	get_other_node (int callers_index) const
	returns a pointer to the other node that the edge is incident upon More...

int	get_first_node_ind () const
	returns the index of the smaller-indexed node More...

int	get_second_node_ind () const
	returns the index of the larger-indexed node More...

void	set_pos_in_owners_list (std::list< EdgeBase * >::iterator edge_iterator)
	edge keeps iterator to its position in it's owner's edge list More...

void	set_pos_in_node_edgevector (int callers_index, int position)
	edge keeps index it has in node_ind's edge vector More...

bool	same_edge (int node1, int node2) const
	returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important More...

Real	edge_weight () const

InteractionGraphBase const *	get_owner () const

InteractionGraphBase *	get_owner ()

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

Private Member Functions
void	handle_bumped_recent_history_state_for_node (int node_substituted, int node_not_substituted, int bumped_recent_history_index)

void	store_curr_state_energy ()

void	wipe (int node)

	SymmLinearMemEdge ()

	SymmLinearMemEdge (SymmLinearMemEdge const &)

SymmLinearMemEdge &	operator= (SymmLinearMemEdge const &)

Private Attributes
bool	store_rpes_ [2]

ObjexxFCL::FArray2D < core::PackerEnergy >	stored_rpes_ [2]

core::PackerEnergy	curr_state_energy_

core::PackerEnergy	alt_state_energy_

bool	partial_state_assignment_

bool	preped_for_sim_annealing_

Additional Inherited Members
Protected Member Functions inherited from core::pack::interaction_graph::SymmOnTheFlyEdge
core::PackerEnergy	get_proline_correction (int which_node, int state) const

SymmOnTheFlyNode const *	get_otf_node (int which_node) const

SymmOnTheFlyNode *	get_otf_node (int which_node)

SymmOnTheFlyInteractionGraph const *	get_otf_owner () const

SymmOnTheFlyInteractionGraph *	get_otf_owner ()

Detailed Description

Definition at line 193 of file SymmLinMemInteractionGraph.hh.

Constructor & Destructor Documentation

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

Definition at line 729 of file SymmLinMemInteractionGraph.cc.

References store_rpes_.

core::pack::interaction_graph::SymmLinearMemEdge::~SymmLinearMemEdge ( )

virtual

Definition at line 742 of file SymmLinMemInteractionGraph.cc.

core::pack::interaction_graph::SymmLinearMemEdge::SymmLinearMemEdge ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

void core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_partial_state_change	(	int	node_ind,
		int	new_state,
		int	bumped_recent_history_index,
		int	new_state_recent_history_index
	)

Definition at line 868 of file SymmLinMemInteractionGraph.cc.

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), get_symmlinmem_node(), handle_bumped_recent_history_state_for_node(), and partial_state_assignment_.

Referenced by core::pack::interaction_graph::SymmLinearMemNode::partial_assign_state().

void core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_state_change	(	int	node_ind,
		int	new_state,
		int	bumped_recent_history_index,
		int	new_state_recent_history_index,
		core::PackerEnergy &	new_energy
	)

Definition at line 816 of file SymmLinMemInteractionGraph.cc.

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), get_symmlinmem_node(), handle_bumped_recent_history_state_for_node(), and store_curr_state_energy().

Referenced by core::pack::interaction_graph::SymmLinearMemNode::assign_state().

void core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_state_zeroed ( int node_ind)

Definition at line 854 of file SymmLinMemInteractionGraph.cc.

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), and get_symmlinmem_node().

void core::pack::interaction_graph::SymmLinearMemEdge::acknowledge_substitution	(	int	substituted_node_index,
		core::PackerEnergy const	curr_state_energy,
		int	nodes_new_state,
		int	bumped_recent_history_index,
		int	new_state_recent_history_index,
		int	neighbors_curr_state
	)

inline

Definition at line 447 of file SymmLinMemInteractionGraph.hh.

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), get_symmlinmem_node(), handle_bumped_recent_history_state_for_node(), and stored_rpes_.

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

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

virtual

Reimplemented from core::pack::interaction_graph::SymmOnTheFlyEdge.

Definition at line 783 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::SymmOnTheFlyEdge::count_dynamic_memory(), and stored_rpes_.

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

virtual

Implements core::pack::interaction_graph::SymmOnTheFlyEdge.

Definition at line 776 of file SymmLinMemInteractionGraph.cc.

References SymmLinearMemEdge().

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

virtual

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

Definition at line 752 of file SymmLinMemInteractionGraph.cc.

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::get_current_two_body_energy ( ) const

Definition at line 809 of file SymmLinMemInteractionGraph.cc.

References curr_state_energy_.

Referenced by core::pack::interaction_graph::SymmLinearMemNode::update_internal_energy_sums().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::get_energy_following_partial_state_assignment ( )

Definition at line 898 of file SymmLinMemInteractionGraph.cc.

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), get_symmlinmem_node(), partial_state_assignment_, and store_curr_state_energy().

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::get_energy_for_alt_state	(	bool	store_rpes,
		int	changing_node_index,
		int	alternate_state,
		int	alternate_state_recent_history_index,
		int	other_node_curr_state,
		int	other_node_state_recent_history_index
	)

Definition at line 938 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::debug, and core::pack::interaction_graph::T().

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

inline

Definition at line 432 of file SymmLinMemInteractionGraph.hh.

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

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

inline

Definition at line 439 of file SymmLinMemInteractionGraph.hh.

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

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

inline

Definition at line 417 of file SymmLinMemInteractionGraph.hh.

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

Referenced by acknowledge_partial_state_change(), acknowledge_state_change(), acknowledge_state_zeroed(), acknowledge_substitution(), get_energy_following_partial_state_assignment(), prepare_for_simulated_annealing(), and store_curr_state_energy().

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

inline

Definition at line 424 of file SymmLinMemInteractionGraph.hh.

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

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

virtual

Implements core::pack::interaction_graph::SymmOnTheFlyEdge.

Definition at line 745 of file SymmLinMemInteractionGraph.cc.

int core::pack::interaction_graph::SymmLinearMemEdge::get_two_body_table_size ( ) const

Definition at line 1020 of file SymmLinMemInteractionGraph.cc.

References core::io::serialization::size(), and stored_rpes_.

void core::pack::interaction_graph::SymmLinearMemEdge::handle_bumped_recent_history_state_for_node	(	int	node_substituted,
		int	node_not_substituted,
		int	bumped_recent_history_index
	)

private

Definition at line 1035 of file SymmLinMemInteractionGraph.cc.

Referenced by acknowledge_partial_state_change(), acknowledge_state_change(), and acknowledge_substitution().

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

private

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

virtual

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

Definition at line 756 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::EdgeBase::get_num_states_for_node(), get_symmlinmem_node(), NOT_YET_COMPUTED_ENERGY, preped_for_sim_annealing_, store_rpes_, stored_rpes_, and wipe().

void core::pack::interaction_graph::SymmLinearMemEdge::print_current_energy ( ) const

Definition at line 1026 of file SymmLinMemInteractionGraph.cc.

References curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_node_index(), and core::pack::interaction_graph::T().

void core::pack::interaction_graph::SymmLinearMemEdge::reset_state_energies	(	int	node_index,
		int	state,
		int	recent_history_id
	)

Definition at line 914 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::EdgeBase::get_node_index(), core::pack::interaction_graph::EdgeBase::get_num_states_for_node(), NOT_YET_COMPUTED_ENERGY, and stored_rpes_.

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

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

virtual

DANGER: this will not update the cached energies on the nodes this edge is incident upon.

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

Definition at line 794 of file SymmLinMemInteractionGraph.cc.

References core::pack::interaction_graph::EdgeBase::edge_weight(), NOT_YET_COMPUTED_ENERGY, and stored_rpes_.

void core::pack::interaction_graph::SymmLinearMemEdge::store_curr_state_energy ( )

private

Definition at line 1050 of file SymmLinMemInteractionGraph.cc.

References curr_state_energy_, core::pack::interaction_graph::SymmLinearMemNode::get_curr_state_recent_state_id(), core::pack::interaction_graph::SymmLinearMemNode::get_current_state(), get_symmlinmem_node(), store_rpes_, and stored_rpes_.

Referenced by acknowledge_state_change(), and get_energy_following_partial_state_assignment().

void core::pack::interaction_graph::SymmLinearMemEdge::wipe ( int node)

private

Definition at line 1070 of file SymmLinMemInteractionGraph.cc.

References NOT_YET_COMPUTED_ENERGY, and stored_rpes_.

Referenced by prepare_for_simulated_annealing().

Member Data Documentation

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::alt_state_energy_

private

Definition at line 291 of file SymmLinMemInteractionGraph.hh.

core::PackerEnergy core::pack::interaction_graph::SymmLinearMemEdge::curr_state_energy_

private

Definition at line 290 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_partial_state_change(), acknowledge_state_change(), acknowledge_state_zeroed(), acknowledge_substitution(), get_current_two_body_energy(), get_energy_following_partial_state_assignment(), print_current_energy(), and store_curr_state_energy().

core::PackerEnergy const core::pack::interaction_graph::SymmLinearMemEdge::NOT_YET_COMPUTED_ENERGY = -1234

static

Definition at line 260 of file SymmLinMemInteractionGraph.hh.

Referenced by prepare_for_simulated_annealing(), reset_state_energies(), set_edge_weight(), and wipe().

bool core::pack::interaction_graph::SymmLinearMemEdge::partial_state_assignment_

private

Definition at line 292 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_partial_state_change(), and get_energy_following_partial_state_assignment().

bool core::pack::interaction_graph::SymmLinearMemEdge::preped_for_sim_annealing_

private

Definition at line 293 of file SymmLinMemInteractionGraph.hh.

Referenced by prepare_for_simulated_annealing().

bool core::pack::interaction_graph::SymmLinearMemEdge::store_rpes_[2]

private

Definition at line 288 of file SymmLinMemInteractionGraph.hh.

Referenced by prepare_for_simulated_annealing(), store_curr_state_energy(), and SymmLinearMemEdge().

ObjexxFCL::FArray2D< core::PackerEnergy > core::pack::interaction_graph::SymmLinearMemEdge::stored_rpes_[2]

private

Definition at line 289 of file SymmLinMemInteractionGraph.hh.

Referenced by acknowledge_substitution(), count_dynamic_memory(), get_two_body_table_size(), prepare_for_simulated_annealing(), reset_state_energies(), set_edge_weight(), store_curr_state_energy(), and wipe().

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

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation