protocols::flexpack::interaction_graph::FlexbbEdge Class Reference

#include <FlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::FlexbbEdge:

Public Types
typedef core::pack::interaction_graph::EdgeBase	parent
typedef core::PackerEnergy	PackerEnergy
typedef core::Real	Real
typedef core::Size	Size

Public Member Functions
	FlexbbEdge (FlexbbInteractionGraph *owner, int first_node_ind, int second_node_ind)
	~FlexbbEdge () override
bool	get_nodes_from_same_flexseg () const
void	set_alt_state (int node_index, int new_state, FlexbbSparseMatrixIndex const &state_info)
	Called by FlexbbNode in prepare_for_bb_jump: Edges must know the alternate states that nodes are considering. Precondition: alt_state_ for a fixed node must match its cur_state_. More...
void	acknowledge_partial_state_assignment (int node_index, int new_state, FlexbbSparseMatrixIndex const &state_info)
void	note_state_substitution_accepted ()
	Copy alt data to current data after a state substitution. More...
void	reset_alternate_states_for_uncommited_substitution ()
	After a rejected state substitution, the FlexbbNode will call this function to reset the alt_state data to establish the invariant that the alternate state held on the flexbb edges reflect the the current state of those nodes not considering a state substitution. More...
unsigned int	count_dynamic_memory () const override
PackerEnergy	cur_energy () const
PackerEnergy	alt_energy () const
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...
virtual void	declare_energies_final ()=0
virtual void	prepare_for_simulated_annealing ()=0
virtual unsigned int	count_static_memory () const =0
Real	edge_weight () const
virtual void	set_edge_weight (Real weight)=0
bool	marked_for_deletion () const
	Has this edge indicated that it can be deleted? More...
InteractionGraphBase const *	get_owner () const
InteractionGraphBase *	get_owner ()

Protected Member Functions
FlexbbNode const *	get_flexbb_node (int index) const
FlexbbNode *	get_flexbb_node (int index)
FlexbbInteractionGraph const *	get_flexbbig_owner () const
FlexbbInteractionGraph *	get_flexbbig_owner ()
int	num_bb (int node)
bool	nodes_part_of_same_flexseg () const
bool	nodes_considering_bb_move () const
void	set_nodes_considering_bb_move (bool status)
int	nodes_cur_state (int node) const
FlexbbSparseMatrixIndex const &	nodes_cur_info (int node) const
int	nodes_alt_state (int node) const
FlexbbSparseMatrixIndex const &	nodes_alt_info (int node) const
bool	alt_e_up_to_date () const
void	set_nodes_cur_state (int node, int setting)
	Set the currently assigned state for a node; node == 0 || 1. More...
void	set_nodes_cur_info (int node, FlexbbSparseMatrixIndex const &setting)
void	set_nodes_alt_state (int node, int setting)
	Set the altnernate state being considered for a node; node == 0 || 1. More...
void	set_nodes_alt_info (int node, FlexbbSparseMatrixIndex const &setting)
void	set_cur_energy (PackerEnergy setting)
void	set_alt_energy (PackerEnergy setting)
void	copy_alternate_to_current ()
void	set_node_state_to_zero (int which_node)
Protected Member Functions inherited from core::pack::interaction_graph::EdgeBase
void	mark_edge_for_deletion ()
	Mark this edge so that it can be deleted. More...
int	get_node_index (int index) const
int	get_num_states_for_node (int index) const
NodeBase const *	get_node (int index) const
NodeBase *	get_node (int index)
int	get_edges_position_in_nodes_edge_vector (int index) const
int	which_node (int node_index) const
	is a node the first or second node this edge is incident upon? More...
void	edge_weight (Real)
	protected setter of the edge weight. To be called by derived classes after they have completed the conversion from the previous edge weighting to the new edge weighting. More...

Private Member Functions
	FlexbbEdge ()
	FlexbbEdge (FlexbbEdge const &)

Private Attributes
bool const	nodes_part_of_same_flexseg_
int	nodes_num_bb_ [2]
int	nodes_cur_state_ [2]
FlexbbSparseMatrixIndex	nodes_cur_info_ [2]
int	nodes_alt_state_ [2]
FlexbbSparseMatrixIndex	nodes_alt_info_ [2]
PackerEnergy	cur_energy_
PackerEnergy	alt_energy_
bool	alt_e_up_to_date_
bool	nodes_considering_bb_move_

Member Typedef Documentation

typedef core::PackerEnergy protocols::flexpack::interaction_graph::FlexbbEdge::PackerEnergy

typedef core::pack::interaction_graph::EdgeBase protocols::flexpack::interaction_graph::FlexbbEdge::parent

typedef core::Real protocols::flexpack::interaction_graph::FlexbbEdge::Real

typedef core::Size protocols::flexpack::interaction_graph::FlexbbEdge::Size

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::FlexbbEdge::FlexbbEdge	(	FlexbbInteractionGraph *	owner,
		int	first_node_ind,
		int	second_node_ind
	)

References get_flexbb_node(), protocols::flexpack::interaction_graph::FlexbbNode::get_num_distinct_backbones(), nodes_alt_state_, nodes_cur_state_, and nodes_num_bb_.

protocols::flexpack::interaction_graph::FlexbbEdge::~FlexbbEdge ( )

overridedefault

protocols::flexpack::interaction_graph::FlexbbEdge::FlexbbEdge ( )

private

protocols::flexpack::interaction_graph::FlexbbEdge::FlexbbEdge ( FlexbbEdge const &  )

private

Member Function Documentation

void protocols::flexpack::interaction_graph::FlexbbEdge::acknowledge_partial_state_assignment	(	int	node_index,
		int	new_state,
		FlexbbSparseMatrixIndex const &	state_info
	)

References alt_e_up_to_date_, alt_energy_, cur_energy_, nodes_alt_info_, nodes_alt_state_, nodes_considering_bb_move_, nodes_cur_info_, nodes_cur_state_, and core::pack::interaction_graph::EdgeBase::which_node().

Referenced by protocols::flexpack::interaction_graph::FlexbbNode::inform_incident_edges_about_partial_state_assignment().

bool protocols::flexpack::interaction_graph::FlexbbEdge::alt_e_up_to_date ( ) const

inlineprotected

References alt_e_up_to_date_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::get_alt_stateE().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbEdge::alt_energy ( ) const

inline

References alt_e_up_to_date_, and alt_energy_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::get_alt_stateE().

void protocols::flexpack::interaction_graph::FlexbbEdge::copy_alternate_to_current ( )

protected

References alt_e_up_to_date_, alt_energy_, cur_energy_, nodes_alt_info_, nodes_alt_state_, nodes_considering_bb_move_, nodes_cur_info_, and nodes_cur_state_.

unsigned int protocols::flexpack::interaction_graph::FlexbbEdge::count_dynamic_memory ( ) const

overridevirtual

Reimplemented from core::pack::interaction_graph::EdgeBase.

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbEdge, and protocols::flexpack::interaction_graph::OTFFlexbbEdge.

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

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::count_dynamic_memory().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbEdge::cur_energy ( ) const

inline

References cur_energy_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_sum_for_vertex_group(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::update_internal_energy_totals().

FlexbbNode const* protocols::flexpack::interaction_graph::FlexbbEdge::get_flexbb_node ( int  index ) const

inlineprotected

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

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), and FlexbbEdge().

FlexbbNode* protocols::flexpack::interaction_graph::FlexbbEdge::get_flexbb_node ( int  index )

inlineprotected

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

FlexbbInteractionGraph const * protocols::flexpack::interaction_graph::FlexbbEdge::get_flexbbig_owner ( ) const

inlineprotected

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

FlexbbInteractionGraph * protocols::flexpack::interaction_graph::FlexbbEdge::get_flexbbig_owner ( )

inlineprotected

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

bool protocols::flexpack::interaction_graph::FlexbbEdge::get_nodes_from_same_flexseg ( ) const

inline

References nodes_part_of_same_flexseg_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), and protocols::flexpack::interaction_graph::FlexbbNode::update_internal_vectors().

FlexbbSparseMatrixIndex const& protocols::flexpack::interaction_graph::FlexbbEdge::nodes_alt_info ( int  node ) const

inlineprotected

References nodes_alt_info_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node().

int protocols::flexpack::interaction_graph::FlexbbEdge::nodes_alt_state ( int  node ) const

inlineprotected

References nodes_alt_state_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::alt_rot(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node().

bool protocols::flexpack::interaction_graph::FlexbbEdge::nodes_considering_bb_move ( ) const

inlineprotected

References nodes_considering_bb_move_.

FlexbbSparseMatrixIndex const& protocols::flexpack::interaction_graph::FlexbbEdge::nodes_cur_info ( int  node ) const

inlineprotected

References nodes_cur_info_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node().

int protocols::flexpack::interaction_graph::FlexbbEdge::nodes_cur_state ( int  node ) const

inlineprotected

References nodes_cur_state_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), and protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::set_edge_weight().

bool protocols::flexpack::interaction_graph::FlexbbEdge::nodes_part_of_same_flexseg ( ) const

inlineprotected

References nodes_part_of_same_flexseg_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::compact_bbindex(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::OTFFlexbbEdge().

void protocols::flexpack::interaction_graph::FlexbbEdge::note_state_substitution_accepted

(

)

Copy alt data to current data after a state substitution.

References alt_energy_, cur_energy_, nodes_alt_info_, nodes_alt_state_, nodes_considering_bb_move_, nodes_cur_info_, and nodes_cur_state_.

Referenced by protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current(), and protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current_following_flexbb_accept().

int protocols::flexpack::interaction_graph::FlexbbEdge::num_bb ( int  node )

inlineprotected

References nodes_num_bb_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::OTFFlexbbEdge(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing().

void protocols::flexpack::interaction_graph::FlexbbEdge::reset_alternate_states_for_uncommited_substitution

(

)

After a rejected state substitution, the FlexbbNode will call this function to reset the alt_state data to establish the invariant that the alternate state held on the flexbb edges reflect the the current state of those nodes not considering a state substitution.

References alt_e_up_to_date_, alt_energy_, cur_energy_, nodes_alt_info_, nodes_alt_state_, nodes_considering_bb_move_, nodes_cur_info_, and nodes_cur_state_.

Referenced by protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_considered_fixedbb_substition_uncommitted(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::resolve_uncommitted_substitution().

void protocols::flexpack::interaction_graph::FlexbbEdge::set_alt_energy ( PackerEnergy  setting )

inlineprotected

References alt_e_up_to_date_, and alt_energy_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node().

void protocols::flexpack::interaction_graph::FlexbbEdge::set_alt_state	(	int	node_index,
		int	alternate_state,
		FlexbbSparseMatrixIndex const &	alt_state_info
	)

Called by FlexbbNode in prepare_for_bb_jump: Edges must know the alternate states that nodes are considering. Precondition: alt_state_ for a fixed node must match its cur_state_.

during backbone-moving rotamer substitutions, the nodes on flexible segments must inform their edges of their new states.

References alt_e_up_to_date_, protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex::get_bb(), nodes_alt_info_, nodes_alt_state_, nodes_considering_bb_move_, nodes_cur_info_, nodes_cur_state_, nodes_part_of_same_flexseg_, and core::pack::interaction_graph::EdgeBase::which_node().

Referenced by protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

void protocols::flexpack::interaction_graph::FlexbbEdge::set_cur_energy ( PackerEnergy  setting )

inlineprotected

References cur_energy_.

void protocols::flexpack::interaction_graph::FlexbbEdge::set_node_state_to_zero ( int  which_node )

protected

References alt_e_up_to_date_, alt_energy_, cur_energy_, nodes_alt_info_, nodes_alt_state_, nodes_considering_bb_move_, nodes_cur_info_, nodes_cur_state_, and core::pack::interaction_graph::EdgeBase::which_node().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_state_zeroed(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::zero_state_on_node().

void protocols::flexpack::interaction_graph::FlexbbEdge::set_nodes_alt_info ( int  node, FlexbbSparseMatrixIndex const &  setting  )

inlineprotected

References nodes_alt_info_.

void protocols::flexpack::interaction_graph::FlexbbEdge::set_nodes_alt_state ( int  node, int  setting  )

inlineprotected

Set the altnernate state being considered for a node; node == 0 || 1.

References nodes_alt_state_.

void protocols::flexpack::interaction_graph::FlexbbEdge::set_nodes_considering_bb_move ( bool  status )

inlineprotected

References nodes_considering_bb_move_.

void protocols::flexpack::interaction_graph::FlexbbEdge::set_nodes_cur_info ( int  node, FlexbbSparseMatrixIndex const &  setting  )

inlineprotected

References nodes_cur_info_.

void protocols::flexpack::interaction_graph::FlexbbEdge::set_nodes_cur_state ( int  node, int  setting  )

inlineprotected

Set the currently assigned state for a node; node == 0 || 1.

References nodes_cur_state_.

Member Data Documentation

bool protocols::flexpack::interaction_graph::FlexbbEdge::alt_e_up_to_date_

private

Referenced by acknowledge_partial_state_assignment(), alt_e_up_to_date(), alt_energy(), copy_alternate_to_current(), reset_alternate_states_for_uncommited_substitution(), set_alt_energy(), set_alt_state(), and set_node_state_to_zero().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbEdge::alt_energy_

private

Referenced by acknowledge_partial_state_assignment(), alt_energy(), copy_alternate_to_current(), note_state_substitution_accepted(), reset_alternate_states_for_uncommited_substitution(), set_alt_energy(), and set_node_state_to_zero().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbEdge::cur_energy_

private

Referenced by acknowledge_partial_state_assignment(), copy_alternate_to_current(), cur_energy(), note_state_substitution_accepted(), reset_alternate_states_for_uncommited_substitution(), set_cur_energy(), and set_node_state_to_zero().

FlexbbSparseMatrixIndex protocols::flexpack::interaction_graph::FlexbbEdge::nodes_alt_info_[2]

private

Referenced by acknowledge_partial_state_assignment(), copy_alternate_to_current(), nodes_alt_info(), note_state_substitution_accepted(), reset_alternate_states_for_uncommited_substitution(), set_alt_state(), set_node_state_to_zero(), and set_nodes_alt_info().

int protocols::flexpack::interaction_graph::FlexbbEdge::nodes_alt_state_[2]

private

Referenced by acknowledge_partial_state_assignment(), copy_alternate_to_current(), FlexbbEdge(), nodes_alt_state(), note_state_substitution_accepted(), reset_alternate_states_for_uncommited_substitution(), set_alt_state(), set_node_state_to_zero(), and set_nodes_alt_state().

bool protocols::flexpack::interaction_graph::FlexbbEdge::nodes_considering_bb_move_

private

Referenced by acknowledge_partial_state_assignment(), copy_alternate_to_current(), nodes_considering_bb_move(), note_state_substitution_accepted(), reset_alternate_states_for_uncommited_substitution(), set_alt_state(), set_node_state_to_zero(), and set_nodes_considering_bb_move().

FlexbbSparseMatrixIndex protocols::flexpack::interaction_graph::FlexbbEdge::nodes_cur_info_[2]

private

Referenced by acknowledge_partial_state_assignment(), copy_alternate_to_current(), nodes_cur_info(), note_state_substitution_accepted(), reset_alternate_states_for_uncommited_substitution(), set_alt_state(), set_node_state_to_zero(), and set_nodes_cur_info().

int protocols::flexpack::interaction_graph::FlexbbEdge::nodes_cur_state_[2]

private

Referenced by acknowledge_partial_state_assignment(), copy_alternate_to_current(), FlexbbEdge(), nodes_cur_state(), note_state_substitution_accepted(), reset_alternate_states_for_uncommited_substitution(), set_alt_state(), set_node_state_to_zero(), and set_nodes_cur_state().

int protocols::flexpack::interaction_graph::FlexbbEdge::nodes_num_bb_[2]

private

Referenced by FlexbbEdge(), and num_bb().

bool const protocols::flexpack::interaction_graph::FlexbbEdge::nodes_part_of_same_flexseg_

private

Referenced by get_nodes_from_same_flexseg(), nodes_part_of_same_flexseg(), and set_alt_state().

---

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

• src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.hh
• src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.cc