#include <FlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::FlexbbNode:

Collaboration diagram for protocols::flexpack::interaction_graph::FlexbbNode:

Public Types
typedef core::pack::interaction_graph::NodeBase	parent

typedef core::PackerEnergy	PackerEnergy

typedef core::Size	Size

Public Member Functions
	FlexbbNode (FlexbbInteractionGraph *owner, int node_id, int num_states)

virtual	~FlexbbNode ()

virtual void	print () const

void	set_num_distinct_backbones (int nbbconfs)

int	get_num_distinct_backbones () const

void	set_num_states_per_backbone (utility::vector1< int > const &)

int	get_bb_for_state (int state) const

int	get_num_states_for_bb (int bbconf) const

int	get_state_offset_for_bb (int bbconf) const

void	get_states_on_curr_bb (utility::vector1< Size > &state_list, int offset) const

void	get_all_states (utility::vector1< Size > &rotlist, int offset) const

void	set_closest_states_on_other_bbs (ObjexxFCL::FArray2D_int const &)

void	set_amino_acid_types (utility::vector1< int > const &)

ObjexxFCL::FArray1A_int	getNumStatesPerAAPerBB (int aa)

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

virtual void	add_to_one_body_energy (int state, PackerEnergy energy)

virtual void	update_one_body_energy (int state, PackerEnergy energy)

virtual void	zero_one_body_energies ()

virtual bool	state_unassigned () const

PackerEnergy	get_one_body_energy (int state) const

virtual void	prepare_for_simulated_annealing ()

int	get_current_state () const

int	get_backbone_for_current_state () const

void	write_current_state_to_state_array (ObjexxFCL::FArray1_int &nodes_states)

bool	inform_edges_of_alt_state_before_bbjump ()
	Preliminatry bookkeeping for the node the Graph contacted about a backbone move. This node is the "root" of the DFS traversal. More...

bool	state_has_same_backbone_as_current (int state) const
	Did the alterenate state assigned during a flexbb move actually preserve the currently assigned bb? More...

int	get_num_states_for_aa_type_for_bb (int aa_type, int bb) const

void	print_internal_energies ()

void	update_internal_energy_sums ()

virtual unsigned int	count_dynamic_memory () const
	memory accounting scheme More...

int	num_aa_types () const
	Read access to private data to both derived classes and the world. More...

int	num_bbconfs () const

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

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

ObjexxFCL::FArray2D_int const &	num_states_for_aa_for_bb ()

ObjexxFCL::FArray2D_int const &	state_offsets_for_aa_for_bb ()

ObjexxFCL::FArray2D_int const &	closest_state_on_alt_bb () const

FlexbbSparseMatrixIndex const &	state_info (int state) const

utility::vector1< PackerEnergy > const &	one_body_energies () const

int	current_state () const

FlexbbSparseMatrixIndex const &	current_state_info () const

int	curr_bb () const

PackerEnergy	curr_state_one_body_energy () const

PackerEnergy	curr_state_total_energy () const

utility::vector1< PackerEnergy > const &	curr_state_two_body_energies ()

int	alternate_state () const

FlexbbSparseMatrixIndex const &	alternate_state_info () const

int	alt_bb () const

PackerEnergy	alternate_state_one_body_energy () const

PackerEnergy	alternate_state_total_energy () const

utility::vector1< PackerEnergy > const &	alternate_state_two_body_energies () const

PackerEnergy	alternate_state_two_body_energies (int ind) const

utility::vector1< bool > const &	edge_connects_flexsegmate () const

bool	count_energy_to_node_in_my_fragtotalE (int edge_index) const
	Convention for acumulating energies between flexsegmates during a backbone move: The smaller-indexed node counts the interaction, the larger-indexed node does not. More...

bool	alternate_state_is_being_considered () const

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...

virtual void	assign_zero_state ()=0

virtual void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b)=0

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...

virtual unsigned int	count_static_memory () const =0

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
FlexbbEdge const *	get_incident_flexbb_edge (int index) const

FlexbbEdge *	get_incident_flexbb_edge (int index)

FlexbbNode const *	get_adjacent_flexbb_node (int index) const

FlexbbNode *	get_adjacent_flexbb_node (int index)

FlexbbInteractionGraph const *	get_flexbbig_owner () const

FlexbbInteractionGraph *	get_flexbbig_owner ()

void	update_internal_vectors ()

void	inform_edges_considered_fixedbb_substition_uncommitted ()

void	set_considering_alternate_state ()
	Limited write acces to private data. More...

void	set_current_state (int setting)

void	set_curr_state_one_body_energy (PackerEnergy setting)

void	set_curr_state_total_energy (PackerEnergy setting)

void	inc_curr_state_total_energy (PackerEnergy setting)

void	set_curr_state_two_body_energies (Size index, PackerEnergy setting)

void	set_alternate_state (int setting)

void	set_alternate_state_one_body_energy (PackerEnergy setting)

void	set_alternate_state_total_energy (PackerEnergy setting)

void	inc_alternate_state_total_energy (PackerEnergy setting)

void	set_alternate_state_two_body_energies (Size index, PackerEnergy setting)

void	reset_all_rotamer_substitution_bookkeeping_data ()

void	partial_state_assignment (int new_state)

void	inform_incident_edges_about_partial_state_assignment ()

void	copy_alternate_to_current ()
	bookkeeping for DFS traversal. Derived classes should consult this at the beginning of node "get_energies" traversals. Calling this function for a node effectively declares that the code which follows will project the delta energy: after the first time this functio is called, it will return true. Must be proceeded by a call to prepare_for_bb_jump(). Depricated. bool energies_already_projected() const; More...

void	have_edges_copy_alternate_to_current ()
	Have all incident edges copy their data from "alternate_" to "current_". More...

void	have_edges_copy_alternate_to_current_following_flexbb_accept ()
	Have a subset of the incident edges copy their data from "alternate_" to "current_" where this subset includes all edges to non-flexsegmates as well as all all upper edges to flexsegmates. Threadsafe if it can be fruitfully parallelized. More...

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 ()

Private Member Functions
	FlexbbNode ()

	FlexbbNode (FlexbbNode const &)

Private Attributes
int	num_aa_types_

int	num_bb_

utility::vector1< int >	num_states_for_bb_

utility::vector1< int >	state_offsets_for_bb_

ObjexxFCL::FArray2D_int	num_states_for_aa_for_bb_

ObjexxFCL::FArray2D_int	state_offsets_for_aa_for_bb_

ObjexxFCL::FArray2D_int	closest_state_on_alt_bb_

utility::vector0 < FlexbbSparseMatrixIndex >	state_info_
	vector0 so that assigning state 0 does not index out-of-bounds. More...

utility::vector1< PackerEnergy >	one_body_energies_

int	current_state_

FlexbbSparseMatrixIndex	current_state_info_

PackerEnergy	curr_state_one_body_energy_

PackerEnergy	curr_state_total_energy_

utility::vector1< PackerEnergy >	curr_state_two_body_energies_

int	alternate_state_

FlexbbSparseMatrixIndex	alternate_state_info_

PackerEnergy	alternate_state_one_body_energy_

PackerEnergy	alternate_state_total_energy_

utility::vector1< PackerEnergy >	alternate_state_two_body_energies_

utility::vector1< bool >	edge_connects_flexsegmate_

bool	alternate_state_is_being_considered_

Detailed Description

Definition at line 44 of file FlexbbInteractionGraph.hh.

Member Typedef Documentation

typedef core::PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::PackerEnergy

Definition at line 48 of file FlexbbInteractionGraph.hh.

typedef core::pack::interaction_graph::NodeBase protocols::flexpack::interaction_graph::FlexbbNode::parent

Definition at line 47 of file FlexbbInteractionGraph.hh.

typedef core::Size protocols::flexpack::interaction_graph::FlexbbNode::Size

Definition at line 49 of file FlexbbInteractionGraph.hh.

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::FlexbbNode::FlexbbNode	(	FlexbbInteractionGraph *	owner,
		int	node_id,
		int	num_states
	)

Definition at line 40 of file FlexbbInteractionGraph.cc.

References core::pack::interaction_graph::NodeBase::get_num_states(), and state_info_.

protocols::flexpack::interaction_graph::FlexbbNode::~FlexbbNode ( )

virtual

Definition at line 68 of file FlexbbInteractionGraph.cc.

protocols::flexpack::interaction_graph::FlexbbNode::FlexbbNode ( )

private

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

private

Member Function Documentation

void protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energies ( ObjexxFCL::FArray1< PackerEnergy > & energies)

virtual

Definition at line 218 of file FlexbbInteractionGraph.cc.

References one_body_energies_.

void protocols::flexpack::interaction_graph::FlexbbNode::add_to_one_body_energy	(	int	state,
		PackerEnergy	energy
	)

virtual

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

Definition at line 228 of file FlexbbInteractionGraph.cc.

References one_body_energies_.

int protocols::flexpack::interaction_graph::FlexbbNode::alt_bb ( ) const

inline

Definition at line 198 of file FlexbbInteractionGraph.hh.

References alternate_state_info_, and protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex::get_bb().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_closest_state().

int protocols::flexpack::interaction_graph::FlexbbNode::alternate_state ( ) const

inline

Definition at line 196 of file FlexbbInteractionGraph.hh.

References alternate_state_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state().

FlexbbSparseMatrixIndex const& protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_info ( ) const

inline

Definition at line 197 of file FlexbbInteractionGraph.hh.

References alternate_state_info_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

bool protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_is_being_considered ( ) const

inline

Definition at line 211 of file FlexbbInteractionGraph.hh.

References alternate_state_is_being_considered_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_one_body_energy ( ) const

inline

Definition at line 201 of file FlexbbInteractionGraph.hh.

References alternate_state_one_body_energy_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_total_energy ( ) const

inline

Definition at line 202 of file FlexbbInteractionGraph.hh.

References alternate_state_total_energy_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

utility::vector1< PackerEnergy > const& protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies ( ) const

inline

Definition at line 203 of file FlexbbInteractionGraph.hh.

References alternate_state_two_body_energies_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies ( int ind) const

inline

Definition at line 204 of file FlexbbInteractionGraph.hh.

References alternate_state_two_body_energies_.

ObjexxFCL::FArray2D_int const& protocols::flexpack::interaction_graph::FlexbbNode::closest_state_on_alt_bb ( ) const

inline

Definition at line 184 of file FlexbbInteractionGraph.hh.

References closest_state_on_alt_bb_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_closest_state(), and set_closest_states_on_other_bbs().

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

protected

bookkeeping for DFS traversal. Derived classes should consult this at the beginning of node "get_energies" traversals. Calling this function for a node effectively declares that the code which follows will project the delta energy: after the first time this functio is called, it will return true. Must be proceeded by a call to prepare_for_bb_jump(). Depricated. bool energies_already_projected() const;

Copy over the energy data local to this node from "alternate_*" to "current_*"

Definition at line 424 of file FlexbbInteractionGraph.cc.

References alternate_state_, alternate_state_info_, 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_, and current_state_info_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment().

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

virtual

memory accounting scheme

Reimplemented from core::pack::interaction_graph::NodeBase.

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbNode, and protocols::flexpack::interaction_graph::OTFFlexbbNode.

Definition at line 334 of file FlexbbInteractionGraph.cc.

References closest_state_on_alt_bb_, core::pack::interaction_graph::NodeBase::count_dynamic_memory(), num_states_for_aa_for_bb_, num_states_for_bb_, and state_offsets_for_bb_.

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

bool protocols::flexpack::interaction_graph::FlexbbNode::count_energy_to_node_in_my_fragtotalE ( int edge_index) const

inline

Convention for acumulating energies between flexsegmates during a backbone move: The smaller-indexed node counts the interaction, the larger-indexed node does not.

Definition at line 210 of file FlexbbInteractionGraph.hh.

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

int protocols::flexpack::interaction_graph::FlexbbNode::curr_bb ( ) const

inline

Definition at line 190 of file FlexbbInteractionGraph.hh.

References current_state_info_, and protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex::get_bb().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_closest_state().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::curr_state_one_body_energy ( ) const

inline

Definition at line 191 of file FlexbbInteractionGraph.hh.

References curr_state_one_body_energy_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_sum_for_vertex_group(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::update_internal_energy_totals().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::curr_state_total_energy ( ) const

inline

Definition at line 192 of file FlexbbInteractionGraph.hh.

References curr_state_total_energy_.

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

utility::vector1< PackerEnergy > const& protocols::flexpack::interaction_graph::FlexbbNode::curr_state_two_body_energies ( )

inline

Definition at line 193 of file FlexbbInteractionGraph.hh.

References curr_state_two_body_energies_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::acknowledge_neighbors_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total().

int protocols::flexpack::interaction_graph::FlexbbNode::current_state ( ) const

inline

Definition at line 188 of file FlexbbInteractionGraph.hh.

References current_state_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_closest_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::resolve_uncommitted_substitution().

FlexbbSparseMatrixIndex const& protocols::flexpack::interaction_graph::FlexbbNode::current_state_info ( ) const

inline

Definition at line 189 of file FlexbbInteractionGraph.hh.

References current_state_info_.

utility::vector1< bool > const& protocols::flexpack::interaction_graph::FlexbbNode::edge_connects_flexsegmate ( ) const

inline

Definition at line 206 of file FlexbbInteractionGraph.hh.

References edge_connects_flexsegmate_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), and have_edges_copy_alternate_to_current_following_flexbb_accept().

FlexbbNode const * protocols::flexpack::interaction_graph::FlexbbNode::get_adjacent_flexbb_node ( int index) const

inlineprotected

Definition at line 659 of file FlexbbInteractionGraph.hh.

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

FlexbbNode * protocols::flexpack::interaction_graph::FlexbbNode::get_adjacent_flexbb_node ( int index)

inlineprotected

Definition at line 663 of file FlexbbInteractionGraph.hh.

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

void protocols::flexpack::interaction_graph::FlexbbNode::get_all_states	(	utility::vector1< Size > &	rotlist,
		int	offset
	)		const

Definition at line 150 of file FlexbbInteractionGraph.cc.

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

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states().

int protocols::flexpack::interaction_graph::FlexbbNode::get_backbone_for_current_state ( ) const

Definition at line 270 of file FlexbbInteractionGraph.cc.

References current_state_, and state_info_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_currently_assigned().

int protocols::flexpack::interaction_graph::FlexbbNode::get_bb_for_state ( int state) const

inline

Definition at line 60 of file FlexbbInteractionGraph.hh.

References state_info_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_bb_for_state(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

int protocols::flexpack::interaction_graph::FlexbbNode::get_current_state ( ) const

Definition at line 264 of file FlexbbInteractionGraph.cc.

References current_state_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::print_current_state_assignment().

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

inlineprotected

Definition at line 668 of file FlexbbInteractionGraph.hh.

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

Referenced by inform_edges_of_alt_state_before_bbjump().

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

inlineprotected

Definition at line 672 of file FlexbbInteractionGraph.hh.

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

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

inlineprotected

Downcast pointers to incident edges, adjacent nodes, and the owning graph ^— Oxford comma. See Vampire Weekend's objection.

Definition at line 651 of file FlexbbInteractionGraph.hh.

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

Referenced by have_edges_copy_alternate_to_current(), have_edges_copy_alternate_to_current_following_flexbb_accept(), inform_edges_considered_fixedbb_substition_uncommitted(), inform_edges_of_alt_state_before_bbjump(), inform_incident_edges_about_partial_state_assignment(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution(), and update_internal_vectors().

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

inlineprotected

Definition at line 655 of file FlexbbInteractionGraph.hh.

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

int protocols::flexpack::interaction_graph::FlexbbNode::get_num_distinct_backbones ( ) const

inline

Definition at line 58 of file FlexbbInteractionGraph.hh.

References num_bb_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), protocols::flexpack::interaction_graph::FlexbbEdge::FlexbbEdge(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_closest_state().

int protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_aa_type_for_bb	(	int	aa_type,
		int	bb
	)		const

In a bbmove, did the backbone actually move? Should be called only by the node who was initially contacted

Definition at line 311 of file FlexbbInteractionGraph.cc.

References num_states_for_aa_for_bb_.

int protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_bb ( int bbconf) const

Definition at line 125 of file FlexbbInteractionGraph.cc.

References num_states_for_bb_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_states_per_backbone_for_node(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

FlexbbNode::PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::get_one_body_energy ( int state) const

Definition at line 252 of file FlexbbInteractionGraph.cc.

References one_body_energies_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_one_body_energy_for_node_state().

int protocols::flexpack::interaction_graph::FlexbbNode::get_state_offset_for_bb ( int bbconf) const

Definition at line 130 of file FlexbbInteractionGraph.cc.

References state_offsets_for_bb_.

void protocols::flexpack::interaction_graph::FlexbbNode::get_states_on_curr_bb	(	utility::vector1< Size > &	state_list,
		int	offset
	)		const

Definition at line 135 of file FlexbbInteractionGraph.cc.

References current_state_, num_states_for_bb_, state_info_, and state_offsets_for_bb_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states().

FArray1A_int protocols::flexpack::interaction_graph::FlexbbNode::getNumStatesPerAAPerBB ( int aa)

Definition at line 211 of file FlexbbInteractionGraph.cc.

References num_states_for_aa_for_bb_.

void protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current ( )

protected

Have all incident edges copy their data from "alternate_*" to "current_*".

Definition at line 441 of file FlexbbInteractionGraph.cc.

References get_incident_flexbb_edge(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and protocols::flexpack::interaction_graph::FlexbbEdge::note_state_substitution_accepted().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment().

void protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current_following_flexbb_accept ( )

protected

Have a subset of the incident edges copy their data from "alternate_*" to "current_*" where this subset includes all edges to non-flexsegmates as well as all all upper edges to flexsegmates. Threadsafe if it can be fruitfully parallelized.

Definition at line 448 of file FlexbbInteractionGraph.cc.

References edge_connects_flexsegmate(), get_incident_flexbb_edge(), 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(), and protocols::flexpack::interaction_graph::FlexbbEdge::note_state_substitution_accepted().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution().

void protocols::flexpack::interaction_graph::FlexbbNode::inc_alternate_state_total_energy ( PackerEnergy setting)

inlineprotected

Definition at line 229 of file FlexbbInteractionGraph.hh.

References alternate_state_total_energy_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

void protocols::flexpack::interaction_graph::FlexbbNode::inc_curr_state_total_energy ( PackerEnergy setting)

inlineprotected

Definition at line 220 of file FlexbbInteractionGraph.hh.

References curr_state_total_energy_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::acknowledge_neighbors_substitution().

void protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_considered_fixedbb_substition_uncommitted ( )

protected

Definition at line 364 of file FlexbbInteractionGraph.cc.

References alternate_state_is_being_considered_, get_incident_flexbb_edge(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and protocols::flexpack::interaction_graph::FlexbbEdge::reset_alternate_states_for_uncommited_substitution().

bool protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump ( )

Preliminatry bookkeeping for the node the Graph contacted about a backbone move. This node is the "root" of the DFS traversal.

Preliminary bookkeeping for DFS-backbone-motion inducing state substitution initiated by a separate node. Returns false if the current state is unassigned.

Edges must be informed of the alternate state for both of their nodes; this should happen before any edge is asked for an alternate-state energy.

Definition at line 285 of file FlexbbInteractionGraph.cc.

References alternate_state_, alternate_state_info_, alternate_state_is_being_considered_, current_state_, get_flexbbig_owner(), get_incident_flexbb_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::increment_count_nodes_in_flexseg(), and protocols::flexpack::interaction_graph::FlexbbEdge::set_alt_state().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state().

void protocols::flexpack::interaction_graph::FlexbbNode::inform_incident_edges_about_partial_state_assignment ( )

protected

Definition at line 415 of file FlexbbInteractionGraph.cc.

References protocols::flexpack::interaction_graph::FlexbbEdge::acknowledge_partial_state_assignment(), current_state_, current_state_info_, get_incident_flexbb_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state().

int protocols::flexpack::interaction_graph::FlexbbNode::num_aa_types ( ) const

inline

Read access to private data to both derived classes and the world.

Definition at line 177 of file FlexbbInteractionGraph.hh.

References num_aa_types_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized().

int protocols::flexpack::interaction_graph::FlexbbNode::num_bbconfs ( ) const

inline

Definition at line 178 of file FlexbbInteractionGraph.hh.

References num_bb_.

ObjexxFCL::FArray2D_int const& protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_aa_for_bb ( )

inline

Definition at line 181 of file FlexbbInteractionGraph.hh.

References num_states_for_aa_for_bb_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized().

utility::vector1< int > const& protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_bb ( )

inline

Definition at line 179 of file FlexbbInteractionGraph.hh.

References num_states_for_bb_.

Referenced by set_num_states_per_backbone().

utility::vector1< PackerEnergy > const& protocols::flexpack::interaction_graph::FlexbbNode::one_body_energies ( ) const

inline

Definition at line 186 of file FlexbbInteractionGraph.hh.

References one_body_energies_.

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

void protocols::flexpack::interaction_graph::FlexbbNode::partial_state_assignment ( int new_state)

protected

Definition at line 399 of file FlexbbInteractionGraph.cc.

References alternate_state_, alternate_state_info_, alternate_state_is_being_considered_, alternate_state_one_body_energy_, alternate_state_total_energy_, current_state_, current_state_info_, one_body_energies_, and state_info_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state().

void protocols::flexpack::interaction_graph::FlexbbNode::prepare_for_simulated_annealing ( )

virtual

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

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbNode.

Definition at line 258 of file FlexbbInteractionGraph.cc.

References update_internal_vectors().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_simulated_annealing().

void protocols::flexpack::interaction_graph::FlexbbNode::print ( ) const

virtual

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

Reimplemented in protocols::flexpack::interaction_graph::OTFFlexbbNode, and protocols::flexpack::interaction_graph::MinimalistFlexbbNode.

Definition at line 71 of file FlexbbInteractionGraph.cc.

References curr_state_one_body_energy_, curr_state_two_body_energies_, current_state_, core::pack::interaction_graph::NodeBase::get_node_index(), num_bb_, and state_info_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbNode::print().

void protocols::flexpack::interaction_graph::FlexbbNode::print_internal_energies ( )

Definition at line 317 of file FlexbbInteractionGraph.cc.

void protocols::flexpack::interaction_graph::FlexbbNode::reset_all_rotamer_substitution_bookkeeping_data ( )

protected

Definition at line 393 of file FlexbbInteractionGraph.cc.

References alternate_state_is_being_considered_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state().

void protocols::flexpack::interaction_graph::FlexbbNode::set_alternate_state ( int setting)

inlineprotected

Definition at line 223 of file FlexbbInteractionGraph.hh.

References alternate_state_, alternate_state_info_, and state_info_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::resolve_uncommitted_substitution().

void protocols::flexpack::interaction_graph::FlexbbNode::set_alternate_state_one_body_energy ( PackerEnergy setting)

inlineprotected

Definition at line 224 of file FlexbbInteractionGraph.hh.

References alternate_state_one_body_energy_.

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

void protocols::flexpack::interaction_graph::FlexbbNode::set_alternate_state_total_energy ( PackerEnergy setting)

inlineprotected

Definition at line 228 of file FlexbbInteractionGraph.hh.

References alternate_state_total_energy_.

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

void protocols::flexpack::interaction_graph::FlexbbNode::set_alternate_state_two_body_energies	(	Size	index,
		PackerEnergy	setting
	)

inlineprotected

Definition at line 230 of file FlexbbInteractionGraph.hh.

References alternate_state_two_body_energies_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

void protocols::flexpack::interaction_graph::FlexbbNode::set_amino_acid_types ( utility::vector1< int > const & aatypes)

Precondition: num bb have already been set.

Definition at line 183 of file FlexbbInteractionGraph.cc.

References core::pack::interaction_graph::NodeBase::get_num_states(), num_states_for_aa_for_bb_, state_info_, and state_offsets_for_aa_for_bb_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_aatypes_for_node().

void protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs ( ObjexxFCL::FArray2D_int const & closest_state_on_alt_bb)

Definition at line 163 of file FlexbbInteractionGraph.cc.

References closest_state_on_alt_bb(), closest_state_on_alt_bb_, core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_states(), num_bb_, state_info_, and protocols::flexpack::interaction_graph::TR().

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_closest_states_on_other_bbs().

void protocols::flexpack::interaction_graph::FlexbbNode::set_considering_alternate_state ( )

inlineprotected

Limited write acces to private data.

Definition at line 216 of file FlexbbInteractionGraph.hh.

References alternate_state_is_being_considered_.

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

void protocols::flexpack::interaction_graph::FlexbbNode::set_curr_state_one_body_energy ( PackerEnergy setting)

inlineprotected

Definition at line 218 of file FlexbbInteractionGraph.hh.

References curr_state_one_body_energy_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state().

void protocols::flexpack::interaction_graph::FlexbbNode::set_curr_state_total_energy ( PackerEnergy setting)

inlineprotected

Definition at line 219 of file FlexbbInteractionGraph.hh.

References curr_state_total_energy_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state().

void protocols::flexpack::interaction_graph::FlexbbNode::set_curr_state_two_body_energies	(	Size	index,
		PackerEnergy	setting
	)

inlineprotected

Definition at line 221 of file FlexbbInteractionGraph.hh.

References curr_state_two_body_energies_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::acknowledge_neighbors_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state().

void protocols::flexpack::interaction_graph::FlexbbNode::set_current_state ( int setting)

inlineprotected

Definition at line 217 of file FlexbbInteractionGraph.hh.

References current_state_, current_state_info_, and state_info_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state().

void protocols::flexpack::interaction_graph::FlexbbNode::set_num_distinct_backbones ( int nbbconfs)

Requires that num_aa_types_ is set first; num_aa_types_ is currently set in the node's ctor.

Definition at line 84 of file FlexbbInteractionGraph.cc.

References closest_state_on_alt_bb_, num_aa_types_, num_bb_, num_states_for_aa_for_bb_, num_states_for_bb_, state_offsets_for_aa_for_bb_, and state_offsets_for_bb_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_num_bb_for_node().

void protocols::flexpack::interaction_graph::FlexbbNode::set_num_states_per_backbone ( utility::vector1< int > const & num_states_for_bb)

precondition: num_bb_ must have been previously set and must be equal to the number of backbones implicitly identified in num_states_for_bb by its size.

Definition at line 101 of file FlexbbInteractionGraph.cc.

References core::pack::interaction_graph::NodeBase::get_num_states(), num_bb_, num_states_for_bb(), num_states_for_bb_, state_info_, and state_offsets_for_bb_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_num_states_per_backbone_for_node().

bool protocols::flexpack::interaction_graph::FlexbbNode::state_has_same_backbone_as_current ( int state) const

inline

Did the alterenate state assigned during a flexbb move actually preserve the currently assigned bb?

Definition at line 107 of file FlexbbInteractionGraph.hh.

References current_state_info_, protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex::get_bb(), and state_info_.

FlexbbSparseMatrixIndex const& protocols::flexpack::interaction_graph::FlexbbNode::state_info ( int state) const

inline

Definition at line 185 of file FlexbbInteractionGraph.hh.

References state_info_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution().

ObjexxFCL::FArray2D_int const& protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_aa_for_bb ( )

inline

Definition at line 182 of file FlexbbInteractionGraph.hh.

References state_offsets_for_aa_for_bb_.

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

utility::vector1< int > const& protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_bb ( )

inline

Definition at line 180 of file FlexbbInteractionGraph.hh.

References state_offsets_for_bb_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

bool protocols::flexpack::interaction_graph::FlexbbNode::state_unassigned ( ) const

virtual

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

Definition at line 246 of file FlexbbInteractionGraph.cc.

References current_state_.

void protocols::flexpack::interaction_graph::FlexbbNode::update_internal_energy_sums ( )

Numerical noise creeps in to the total_energy as energies are added and subtracted due to neighbors accepting rotamer substitutions.

Definition at line 325 of file FlexbbInteractionGraph.cc.

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

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::update_internal_energy_totals().

void protocols::flexpack::interaction_graph::FlexbbNode::update_internal_vectors ( )

protected

Definition at line 345 of file FlexbbInteractionGraph.cc.

References alternate_state_two_body_energies_, curr_state_two_body_energies_, edge_connects_flexsegmate_, get_incident_flexbb_edge(), protocols::flexpack::interaction_graph::FlexbbEdge::get_nodes_from_same_flexseg(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and core::pack::interaction_graph::NodeBase::update_edge_vector().

Referenced by prepare_for_simulated_annealing().

void protocols::flexpack::interaction_graph::FlexbbNode::update_one_body_energy	(	int	state,
		PackerEnergy	energy
	)

virtual

Setter. This function is not called anywhere and should be removed...

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

Definition at line 236 of file FlexbbInteractionGraph.cc.

References one_body_energies_.

void protocols::flexpack::interaction_graph::FlexbbNode::write_current_state_to_state_array ( ObjexxFCL::FArray1_int & nodes_states)

Definition at line 276 of file FlexbbInteractionGraph.cc.

References current_state_, and core::pack::interaction_graph::NodeBase::get_node_index().

void protocols::flexpack::interaction_graph::FlexbbNode::zero_one_body_energies ( )

virtual

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

Definition at line 241 of file FlexbbInteractionGraph.cc.

References one_body_energies_.

Member Data Documentation

int protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_

private

Definition at line 278 of file FlexbbInteractionGraph.hh.

Referenced by alternate_state(), copy_alternate_to_current(), inform_edges_of_alt_state_before_bbjump(), partial_state_assignment(), and set_alternate_state().

FlexbbSparseMatrixIndex protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_info_

private

Definition at line 279 of file FlexbbInteractionGraph.hh.

Referenced by alt_bb(), alternate_state_info(), copy_alternate_to_current(), inform_edges_of_alt_state_before_bbjump(), partial_state_assignment(), and set_alternate_state().

bool protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_is_being_considered_

private

Definition at line 286 of file FlexbbInteractionGraph.hh.

Referenced by alternate_state_is_being_considered(), copy_alternate_to_current(), inform_edges_considered_fixedbb_substition_uncommitted(), inform_edges_of_alt_state_before_bbjump(), partial_state_assignment(), reset_all_rotamer_substitution_bookkeeping_data(), and set_considering_alternate_state().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_one_body_energy_

private

Definition at line 280 of file FlexbbInteractionGraph.hh.

Referenced by alternate_state_one_body_energy(), copy_alternate_to_current(), partial_state_assignment(), and set_alternate_state_one_body_energy().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_total_energy_

private

Definition at line 281 of file FlexbbInteractionGraph.hh.

Referenced by alternate_state_total_energy(), copy_alternate_to_current(), inc_alternate_state_total_energy(), partial_state_assignment(), and set_alternate_state_total_energy().

utility::vector1< PackerEnergy > protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies_

private

Definition at line 282 of file FlexbbInteractionGraph.hh.

Referenced by alternate_state_two_body_energies(), copy_alternate_to_current(), set_alternate_state_two_body_energies(), and update_internal_vectors().

ObjexxFCL::FArray2D_int protocols::flexpack::interaction_graph::FlexbbNode::closest_state_on_alt_bb_

private

Definition at line 264 of file FlexbbInteractionGraph.hh.

Referenced by closest_state_on_alt_bb(), count_dynamic_memory(), set_closest_states_on_other_bbs(), and set_num_distinct_backbones().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::curr_state_one_body_energy_

private

Definition at line 274 of file FlexbbInteractionGraph.hh.

Referenced by copy_alternate_to_current(), curr_state_one_body_energy(), print(), set_curr_state_one_body_energy(), and update_internal_energy_sums().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbNode::curr_state_total_energy_

private

Definition at line 275 of file FlexbbInteractionGraph.hh.

Referenced by copy_alternate_to_current(), curr_state_total_energy(), inc_curr_state_total_energy(), set_curr_state_total_energy(), and update_internal_energy_sums().

utility::vector1< PackerEnergy > protocols::flexpack::interaction_graph::FlexbbNode::curr_state_two_body_energies_

private

Definition at line 276 of file FlexbbInteractionGraph.hh.

Referenced by copy_alternate_to_current(), curr_state_two_body_energies(), print(), set_curr_state_two_body_energies(), update_internal_energy_sums(), and update_internal_vectors().

int protocols::flexpack::interaction_graph::FlexbbNode::current_state_

private

Definition at line 272 of file FlexbbInteractionGraph.hh.

Referenced by copy_alternate_to_current(), current_state(), get_backbone_for_current_state(), get_current_state(), get_states_on_curr_bb(), inform_edges_of_alt_state_before_bbjump(), inform_incident_edges_about_partial_state_assignment(), partial_state_assignment(), print(), set_current_state(), state_unassigned(), and write_current_state_to_state_array().

FlexbbSparseMatrixIndex protocols::flexpack::interaction_graph::FlexbbNode::current_state_info_

private

Definition at line 273 of file FlexbbInteractionGraph.hh.

Referenced by copy_alternate_to_current(), curr_bb(), current_state_info(), inform_incident_edges_about_partial_state_assignment(), partial_state_assignment(), set_current_state(), and state_has_same_backbone_as_current().

utility::vector1< bool > protocols::flexpack::interaction_graph::FlexbbNode::edge_connects_flexsegmate_

private

Definition at line 284 of file FlexbbInteractionGraph.hh.

Referenced by edge_connects_flexsegmate(), and update_internal_vectors().

int protocols::flexpack::interaction_graph::FlexbbNode::num_aa_types_

private

Definition at line 257 of file FlexbbInteractionGraph.hh.

Referenced by num_aa_types(), and set_num_distinct_backbones().

int protocols::flexpack::interaction_graph::FlexbbNode::num_bb_

private

Definition at line 258 of file FlexbbInteractionGraph.hh.

Referenced by get_num_distinct_backbones(), num_bbconfs(), print(), set_closest_states_on_other_bbs(), set_num_distinct_backbones(), and set_num_states_per_backbone().

ObjexxFCL::FArray2D_int protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_aa_for_bb_

private

Definition at line 262 of file FlexbbInteractionGraph.hh.

Referenced by count_dynamic_memory(), get_num_states_for_aa_type_for_bb(), getNumStatesPerAAPerBB(), num_states_for_aa_for_bb(), set_amino_acid_types(), and set_num_distinct_backbones().

utility::vector1< int > protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_bb_

private

Definition at line 260 of file FlexbbInteractionGraph.hh.

Referenced by count_dynamic_memory(), get_num_states_for_bb(), get_states_on_curr_bb(), num_states_for_bb(), set_num_distinct_backbones(), and set_num_states_per_backbone().

utility::vector1< PackerEnergy > protocols::flexpack::interaction_graph::FlexbbNode::one_body_energies_

private

Definition at line 270 of file FlexbbInteractionGraph.hh.

Referenced by add_to_one_body_energies(), add_to_one_body_energy(), get_one_body_energy(), one_body_energies(), partial_state_assignment(), update_one_body_energy(), and zero_one_body_energies().

utility::vector0< FlexbbSparseMatrixIndex > protocols::flexpack::interaction_graph::FlexbbNode::state_info_

private

vector0 so that assigning state 0 does not index out-of-bounds.

Definition at line 267 of file FlexbbInteractionGraph.hh.

Referenced by FlexbbNode(), get_backbone_for_current_state(), get_bb_for_state(), get_states_on_curr_bb(), partial_state_assignment(), print(), set_alternate_state(), set_amino_acid_types(), set_closest_states_on_other_bbs(), set_current_state(), set_num_states_per_backbone(), state_has_same_backbone_as_current(), and state_info().

ObjexxFCL::FArray2D_int protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_aa_for_bb_

private

Definition at line 263 of file FlexbbInteractionGraph.hh.

Referenced by set_amino_acid_types(), set_num_distinct_backbones(), and state_offsets_for_aa_for_bb().

utility::vector1< int > protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_bb_

private

Definition at line 261 of file FlexbbInteractionGraph.hh.

Referenced by count_dynamic_memory(), get_state_offset_for_bb(), get_states_on_curr_bb(), set_num_distinct_backbones(), set_num_states_per_backbone(), and state_offsets_for_bb().

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

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation