protocols::flexpack::interaction_graph::FlexbbNode Class Reference

#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_

Member Typedef Documentation

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

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

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

Constructor & Destructor Documentation

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

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

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

virtual

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

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.

References one_body_energies_.

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

inline

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

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

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

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

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

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

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

References alternate_state_two_body_energies_.

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

inline

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_*"

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.

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.

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

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

inline

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

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

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

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

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

References current_state_info_.

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

inline

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

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

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

inlineprotected

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

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

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

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

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

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

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.

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

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

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

inline

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

References num_states_for_aa_for_bb_.

int protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_bb

(

int

bbconf)

const

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

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

References state_offsets_for_bb_.

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

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)

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_*".

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.

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

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

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

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.

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

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.

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

References num_bb_.

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

inline

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

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

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

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.

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.

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

(

)

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

protected

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

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

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

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

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.

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)

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.

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

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

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

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

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.

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.

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?

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

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

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

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.

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.

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

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.

References one_body_energies_.

void protocols::flexpack::interaction_graph::FlexbbNode::write_current_state_to_state_array

(

ObjexxFCL::FArray1_int &

nodes_states)

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.

References one_body_energies_.

Member Data Documentation

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

private

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

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

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

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

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

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

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

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

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

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

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

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

Referenced by edge_connects_flexsegmate(), and update_internal_vectors().

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

private

Referenced by num_aa_types(), and set_num_distinct_backbones().

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

private

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

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

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

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.

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

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

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().

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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