#include <SymmMinimalistInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SymmMinimalistEdge:

Collaboration diagram for core::pack::interaction_graph::SymmMinimalistEdge:

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

virtual	~SymmMinimalistEdge ()

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, core::PackerEnergy &new_energy)

void	acknowledge_state_zeroed (int node_ind)

void	acknowledge_partial_state_change (int node_ind, int new_state)

core::PackerEnergy	get_energy_following_partial_state_assignment ()

core::PackerEnergy	get_energy_for_alt_state (int changing_node_index)

core::PackerEnergy	curr_state_energy () const

core::PackerEnergy	alt_state_energy () const

void	acknowledge_substitution (int substituted_node_index, core::PackerEnergy const curr_state_energy, int nodes_new_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)

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 ()

Private Member Functions
SymmMinimalistNode const *	get_symmin_node (int index) const

SymmMinimalistNode *	get_symmin_node (int index)

SymmMinimalistInteractionGraph const *	get_symmin_ig_owner () const

SymmMinimalistInteractionGraph *	get_symmin_ig_owner ()

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)

	SymmMinimalistEdge ()

	SymmMinimalistEdge (SymmMinimalistEdge const &)

SymmMinimalistEdge &	operator= (SymmMinimalistEdge const &)

Private Attributes
bool	store_rpes_ [2]

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

ObjexxFCL::FArray2D< unsigned char >	sparse_aa_neighbors_

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 168 of file SymmMinimalistInteractionGraph.hh.

Constructor & Destructor Documentation

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

Definition at line 620 of file SymmMinimalistInteractionGraph.cc.

core::pack::interaction_graph::SymmMinimalistEdge::~SymmMinimalistEdge ( )

virtual

Definition at line 632 of file SymmMinimalistInteractionGraph.cc.

core::pack::interaction_graph::SymmMinimalistEdge::SymmMinimalistEdge ( )

private

Referenced by count_static_memory().

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

private

Member Function Documentation

void core::pack::interaction_graph::SymmMinimalistEdge::acknowledge_partial_state_change	(	int	node_ind,
		int	new_state
	)

Definition at line 720 of file SymmMinimalistInteractionGraph.cc.

References core::pack::interaction_graph::SymmMinimalistNode::acknowledge_neighbors_partial_state_substitution(), curr_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), get_symmin_node(), and partial_state_assignment_.

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

void core::pack::interaction_graph::SymmMinimalistEdge::acknowledge_state_change	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	new_energy
	)

Definition at line 680 of file SymmMinimalistInteractionGraph.cc.

References core::pack::interaction_graph::SymmMinimalistNode::acknowledge_neighbors_state_substitution(), 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_symmin_node().

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

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

Definition at line 704 of file SymmMinimalistInteractionGraph.cc.

References core::pack::interaction_graph::SymmMinimalistNode::acknowledge_neighbors_state_substitution(), 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_symmin_node().

void core::pack::interaction_graph::SymmMinimalistEdge::acknowledge_substitution	(	int	substituted_node_index,
		core::PackerEnergy const	curr_state_energy,
		int	nodes_new_state
	)

inline

Definition at line 403 of file SymmMinimalistInteractionGraph.hh.

References core::pack::interaction_graph::SymmMinimalistNode::acknowledge_neighbors_state_substitution(), curr_state_energy(), 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_symmin_node().

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

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistEdge::alt_state_energy ( ) const

inline

Definition at line 207 of file SymmMinimalistInteractionGraph.hh.

References alt_state_energy_.

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

virtual

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

Definition at line 659 of file SymmMinimalistInteractionGraph.cc.

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

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

virtual

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

Definition at line 652 of file SymmMinimalistInteractionGraph.cc.

References SymmMinimalistEdge().

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistEdge::curr_state_energy ( ) const

inline

Definition at line 206 of file SymmMinimalistInteractionGraph.hh.

References curr_state_energy_.

Referenced by acknowledge_substitution().

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

virtual

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

Definition at line 641 of file SymmMinimalistInteractionGraph.cc.

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

Definition at line 673 of file SymmMinimalistInteractionGraph.cc.

References curr_state_energy_.

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

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

Definition at line 738 of file SymmMinimalistInteractionGraph.cc.

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

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistEdge::get_energy_for_alt_state ( int changing_node_index)

Definition at line 753 of file SymmMinimalistInteractionGraph.cc.

References alt_state_energy_, core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector(), core::pack::interaction_graph::EdgeBase::get_node_index(), and get_symmin_node().

SymmMinimalistInteractionGraph const * core::pack::interaction_graph::SymmMinimalistEdge::get_symmin_ig_owner ( ) const

inlineprivate

Definition at line 388 of file SymmMinimalistInteractionGraph.hh.

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

SymmMinimalistInteractionGraph * core::pack::interaction_graph::SymmMinimalistEdge::get_symmin_ig_owner ( )

inlineprivate

Definition at line 395 of file SymmMinimalistInteractionGraph.hh.

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

SymmMinimalistNode const * core::pack::interaction_graph::SymmMinimalistEdge::get_symmin_node ( int index) const

inlineprivate

Definition at line 373 of file SymmMinimalistInteractionGraph.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(), and get_energy_for_alt_state().

SymmMinimalistNode * core::pack::interaction_graph::SymmMinimalistEdge::get_symmin_node ( int index)

inlineprivate

Definition at line 380 of file SymmMinimalistInteractionGraph.hh.

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

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

virtual

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

Definition at line 634 of file SymmMinimalistInteractionGraph.cc.

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

Definition at line 765 of file SymmMinimalistInteractionGraph.cc.

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

private

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

private

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

virtual

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

Definition at line 645 of file SymmMinimalistInteractionGraph.cc.

References preped_for_sim_annealing_.

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

Definition at line 771 of file SymmMinimalistInteractionGraph.cc.

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

void core::pack::interaction_graph::SymmMinimalistEdge::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 667 of file SymmMinimalistInteractionGraph.cc.

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

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

private

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

private

Member Data Documentation

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistEdge::alt_state_energy_

private

Definition at line 249 of file SymmMinimalistInteractionGraph.hh.

Referenced by alt_state_energy(), and get_energy_for_alt_state().

core::PackerEnergy core::pack::interaction_graph::SymmMinimalistEdge::curr_state_energy_

private

Definition at line 248 of file SymmMinimalistInteractionGraph.hh.

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

bool core::pack::interaction_graph::SymmMinimalistEdge::partial_state_assignment_

private

Definition at line 250 of file SymmMinimalistInteractionGraph.hh.

Referenced by acknowledge_partial_state_change(), and get_energy_following_partial_state_assignment().

bool core::pack::interaction_graph::SymmMinimalistEdge::preped_for_sim_annealing_

private

Definition at line 251 of file SymmMinimalistInteractionGraph.hh.

Referenced by prepare_for_simulated_annealing().

ObjexxFCL::FArray2D< unsigned char > core::pack::interaction_graph::SymmMinimalistEdge::sparse_aa_neighbors_

private

Definition at line 247 of file SymmMinimalistInteractionGraph.hh.

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

private

Definition at line 245 of file SymmMinimalistInteractionGraph.hh.

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

private

Definition at line 246 of file SymmMinimalistInteractionGraph.hh.

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation