#include <MinimalistFlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph:

Public Types
typedef OTFFlexbbInteractionGraph	parent

Public Types inherited from protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
typedef FlexbbInteractionGraph	parent

typedef core::Real	Real

typedef core::pose::PoseOP	PoseOP

typedef core::pose::PoseCOP	PoseCOP

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::scoring::ScoreFunction	ScoreFunction

Public Types inherited from protocols::flexpack::interaction_graph::FlexbbInteractionGraph
enum	Subsitution { SC_ONLY, BOTH_SC_AND_BB }

typedef core::pack::interaction_graph::InteractionGraphBase	parent

typedef core::PackerEnergy	PackerEnergy

typedef core::pack::interaction_graph::EdgeBase	EdgeBase

Public Member Functions
	MinimalistFlexbbInteractionGraph (int num_nodes)
	GRAPH. More...

	~MinimalistFlexbbInteractionGraph () override

void	initialize (core::pack_basic::RotamerSetsBase const &rot_sets) override
	Virtual functions from InteractionGraphBase. More...

PackerEnergy	get_one_body_energy_for_node_state (int node, int state) override

void	blanket_assign_state_0 () override
	State initialization. More...

PackerEnergy	set_state_for_node (int node_ind, int new_state) override
	Explicit state modification for a node. More...

PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states) override
	Explicit state modification for the network. More...

void	consider_substitution (int node_ind, int new_state, PackerEnergy &delta_energy, PackerEnergy &prev_energy_for_node) override
	Consider switching node "node_ind" to state "new_state". More...

PackerEnergy	commit_considered_substitution () override
	Accept a considered substitution (i.e. make the substitution permanent; commit it). More...

PackerEnergy	get_energy_current_state_assignment () override
	Get the energy resulting from the current set of state assignments. More...

int	get_edge_memory_usage () const override

void	print_current_state_assignment () const override

void	set_errorfull_deltaE_threshold (PackerEnergy deltaE) override

PackerEnergy	get_energy_sum_for_vertex_group (int group_id) override

void	consider_backbone_move (int bb_id, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_flexseg_energy, bool &valid_motion, int &num_nodes_changing_state) override
	Virtual functions from FlexbbInteractionGraph. More...

void	consider_bbmove_w_state_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_flexseg, bool &valid_motion, int &num_nodes_changing_state) override

Public Member Functions inherited from protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
	OTFFlexbbInteractionGraph (int num_nodes)
	GRAPH. More...

	~OTFFlexbbInteractionGraph () override

void	initialize (core::pack_basic::RotamerSetsBase const &) override

void	set_ProCorrection_values_for_edge (int node1, int node2, int node_not_necessarily_proline, int state, int other_bb, PackerEnergy bb_nonprobb_E, PackerEnergy bb_probb_E, PackerEnergy sc_nonprobb_E, PackerEnergy sc_probb_E)

void	set_GlyCorrection_values_for_edge (int node1, int node2, int node_not_necessarily_glycine, int state, int other_bb, PackerEnergy bb_nonglybb_E, PackerEnergy bb_glybb_E, PackerEnergy sc_nonglybb_E, PackerEnergy sc_glybb_E)

unsigned int	count_dynamic_memory () const override

virtual void	set_pose (Pose const &pose)
	Pose must be set before any edges are added to the graph. More...

virtual void	set_scorefxn (ScoreFunction const &sfxn)
	Score function must be set before any edges are added to the graph. More...

PoseCOP	get_pose () const
	Edges request the pose and the score function at the time of their creation. More...

ScoreFunctionCOP	get_scorefxn () const

void	note_long_range_interactions_exist_for_edge (int node1, int node2)
	Informs the edge connecting nodes 1 and 2 that they require long range interactions. Note – the edge must already exist. More...

void	debug_note_considered_substitution (core::conformation::Residue const &alt_rotamer, int index)

void	debug_note_projected_deltaE_of_considered_substitution (PackerEnergy deltaE, PackerEnergy node_alt_total, bool require_match=true)

void	debug_note_accepted_substitution ()

void	debug_note_rejected_substitution ()

Public Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbInteractionGraph
	~FlexbbInteractionGraph () override
	GRAPH. More...

	FlexbbInteractionGraph (int num_nodes)

int	get_num_aa_types () const

utility::vector1< core::Size > const &	flexseg_members (int flexseg) const

int	get_flexseg_for_bb (int bb) const

int	get_flexseg_bb_offset (int flexseg_id) const

bool	nodes_from_same_flexseg (int node1, int node2) const

int	get_num_states_per_backbone_for_node (int node, int bb) const

int	get_bb_for_state (int node, int state) const

void	get_accessible_states (Subsitution move_mode, utility::vector1< core::Size > &rotlist) const

void	get_backbone_list (utility::vector1< core::Size > &bblist) const

bool	get_backbone_currently_assigned (int bbid) const
	Is the backbone conformation (in the global enumertion of backbone conformations) already assigned to the network? False if any residue on the flexible segment that this bbid corresponds to is assigned state 0. More...

bool	get_enforce_bb_contiguity () const
	FlexbbNodes will ask: am I allowed to have a state that breaks the backbone? There are brief periods when the backbone is "broken" as the graph assigns new states to nodes on the same flexible segment. More...

void	increment_count_nodes_in_flexseg ()
	Owner keeps a count of the number of nodes undergoing a simultaneous rotamer substitution as the backbone moves. More...

Public Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase
	~InteractionGraphBase () override
	destructor More...

	InteractionGraphBase (int num_nodes)
	main constructor More...

int	get_num_nodes () const override
	Get the number of nodes in the graph. More...

void	set_num_states_for_node (int node, int num_states)
	sets the number of states for a node of a particular index NEW REQUIREMENT: Nodes must have their num-states set in ascending order by node index; that is, node 1 must go first, node 2 next, and so on. More...

int	get_num_states_for_node (int node) const override
	returns the number of states for a particular node More...

int	get_num_total_states () const override
	Get the total number of states. More...

void	add_edge (int node1, int node2)
	creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order More...

bool	get_edge_exists (int node1, int node2) const
	returns true if an edge between node1 and node2 exists More...

void	drop_all_edges_for_node (int node)
	deletes all edges adjacent to the node specified More...

void	print_vertices () const
	calls print() on each of the nodes in the graph More...

virtual void	print () const

void	output_connectivity (std::ostream &os) const
	writes out a list of all the edges in the graph More...

void	output_dimacs (std::ostream &os) const
	writes out a connectivity description of the graph in the famous dimacs format. (where the first column "DIMACS:" should be sed'ed out) More...

void	set_onebody_energies_multithreaded (core::Size const node_index, core::pack::rotamer_set::RotamerSetCOP rotset, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_assignments)
	Compute and store the onebody energy for all rotamers at a position. Safe for a multithreaded context. More...

void	prepare_graph_for_simulated_annealing () override
	iterate across edges and nodes and allow them to prepare for simulated annealing More...

void	set_edge_weight (int node1, int node2, Real edge_weight)

Real	get_edge_weight (int node1, int node2) const

bool	any_vertex_state_unassigned () const override
	Returns true if any node in the graph is in state 0, the unassigned state. More...

void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &one_body_energies)
	takes one FArray of energies – one energy for each state for each node More...

void	update_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &old_energy1b, ObjexxFCL::FArray1< core::PackerEnergy > &new_energy1b)
	decrements the one body energies by the values held in old_energy1b, increments the one body energies by the values held in new_energy1b, and copies new_energy1b into old_energy1b. More...

void	zero_one_body_energies_for_node (int node)

void	add_to_nodes_one_body_energy (int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies)

void	add_to_nodes_one_body_energy (int node_ind, ObjexxFCL::FArray1< core::PackerEnergy > const &one_body_energies)

void	add_to_nodes_one_body_energy (int node_ind, int state_id, core::PackerEnergy const one_body_energy)
	interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy More...

void	set_number_of_energy_sum_vertex_groups (int num_groups)
	a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More...

void	set_vertex_member_of_group (int vertex, int group)
	a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More...

void	print_vertex_groups ()

int	count_connected_components_and_initialize_vertex_groups ()
	makes a depth first traversal of the graph, counting the number of connected components, and initializes the vertex group memberships to reflect the connected components. Returns the number of connected components in the graph. More...

void	note_vertex_reached (int node_index)
	marks a vertex as belonging to the connected component currently being traversed in the depth first traversal. More...

bool	vertex_already_reached (int node_index)
	used by class NodeBase during the depth-first traversal to determine the number of connected components in the graph. returns true if the dft has already reached the node. More...

bool	get_vertex_member_of_energy_sum_group (int node_index, int group_id)

virtual unsigned int	getTotalMemoryUsage () const

void	reset_edge_list_iterator_for_node (int node_index) const
	set the Graph's (single) edge list iterator to the beginning of the edge list for a particular node More...

void	increment_edge_list_iterator () const
	increment the (single) edge list iterator to the next element More...

bool	edge_list_iterator_at_end () const
	test: have we arrived at the edge list end? More...

EdgeBase const &	get_edge () const
	return a const reference to an edge pointed at by the list iterator More...

virtual void	declare_all_edge_energies_final ()
	Iterates over all edges and calls declare_energies_final() on all of them. Takes O(N) time, where N is the number of edges. More...

EdgeBase const *	find_edge (int node1, int node2, bool const use_threadsafe_lookup=false) const
	Find an edge and return a const pointer to it. More...

EdgeBase *	find_edge (int node1, int node2, bool const use_threadsafe_lookup=false)
	Find an edge and return a nonconst pointer to it. More...

NodeBase *	get_node (int index) const

int	get_num_edges () const

std::list< EdgeBase * >::iterator	get_edge_list_begin ()

std::list< EdgeBase * >::iterator	get_edge_list_end ()

std::list< EdgeBase * > ::const_iterator	get_edge_list_begin () const

std::list< EdgeBase * > ::const_iterator	get_edge_list_end () const

Public Member Functions inherited from core::pack::interaction_graph::AnnealableGraphBase
	AnnealableGraphBase ()
	Constructor. More...

	AnnealableGraphBase (AnnealableGraphBase const &src)
	Copy constructor. More...

	~AnnealableGraphBase () override
	Destructor. More...

virtual void	clean_up_after_packing (core::pose::Pose &pose)
	Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing. More...

Protected Member Functions
void	complete_deltaE_prediction_for_bbmove (core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_flexseg, bool &valid_motion, int &num_nodes_changing_state)

MinimalistFlexbbNode const *	get_minimalistflexbb_node (int index) const
	Downcasts. More...

MinimalistFlexbbNode *	get_minimalistflexbb_node (int index)

MinimalistFlexbbEdge const *	find_minimalist_flexbb_edge (int node1, int node2) const

MinimalistFlexbbEdge *	find_minimalist_flexbb_edge (int node1, int node2)

MinimalistFlexbbEdge const *	cast_minimalist_flexbb_edge (EdgeBase const *edge) const

MinimalistFlexbbEdge *	cast_minimalist_flexbb_edge (EdgeBase *edge)

unsigned int	count_static_memory () const override
	Virtual functions from InteractionGraphBase. More...

unsigned int	count_dynamic_memory () const override

core::pack::interaction_graph::NodeBase *	create_new_node (int node_index, int num_states) override

core::pack::interaction_graph::EdgeBase *	create_new_edge (int index1, int index2) override

void	resolve_uncommitted_substitution ()

Protected Member Functions inherited from protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
OTFFlexbbNode const *	get_otfflexbb_node (int index) const
	Downcasts. More...

OTFFlexbbNode *	get_otfflexbb_node (int index)

OTFFlexbbEdge const *	find_otfflexbb_edge (int node1, int node2) const

OTFFlexbbEdge *	find_otfflexbb_edge (int node1, int node2)

OTFFlexbbEdge const *	cast_otfflexbb_edge (EdgeBase const *edge) const

OTFFlexbbEdge *	cast_otfflexbb_edge (EdgeBase *edge)

Protected Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbInteractionGraph
FlexbbNode const *	get_flexbb_node (int index) const
	Downcasts. More...

FlexbbNode *	get_flexbb_node (int index)

FlexbbEdge const *	find_flexbb_edge (int node1, int node2) const

FlexbbEdge *	find_flexbb_edge (int node1, int node2)

FlexbbEdge const *	cast_flexbb_edge (EdgeBase const *edge) const

FlexbbEdge *	cast_flexbb_edge (EdgeBase *edge)

void	set_enforce_bb_contiguity (bool)

void	note_bbjump_substitution ()

void	note_fixedbb_substitution ()

bool	last_considered_substitution_kept_backbone_fixed () const

bool	last_considered_substitution_moved_the_backbone () const

bool	last_considered_backbone_sub_unresolved () const

bool	last_considered_substitution_unresolved () const

void	note_last_considered_substitution_resolved ()

void	reset_node_in_moving_flexseg_count ()

int	get_num_nodes_changing_state () const

PackerEnergy	total_energy_current_state_assignment () const

PackerEnergy	total_energy_alternate_state_assignment () const

int	node_considering_alt_state () const
	Only allowed to ask for the node considering an alternate state during a fixed-backbone substitution. More...

int	flexseg_considering_alt_bb () const
	Only allowed to ask for the flexible segment considering an alternate backbone conformation during a backbone-moving substitution. More...

bool	last_considered_backbone_sub_valid () const

int	flexseg_for_moltenres (int moltenres) const

void	set_total_energy_current_state_assignment (PackerEnergy setting)

void	set_total_energy_alternate_state_assignment (PackerEnergy setting)

void	set_node_considering_alt_state (int setting)
	Track the last node at which a fixed-backbone substitution took place. More...

void	set_flexseg_considering_alt_bb (int setting)
	Track the last flexible segment at which a moving-backbone substitution took place. More...

void	set_last_considered_backbone_sub_valid (bool setting)

virtual void	update_internal_energy_totals ()

Protected Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase
void	clean_up_edges_marked_for_deletion ()
	Remove those edges that have marked themselves for deletion. More...

void	drop_edge (std::list< EdgeBase * >::iterator edge)
	removes edge from edge list at iterator iter More...

int	get_node_state_offset (int index) const

bool	mine (EdgeBase const *edge) const

Private Member Functions
PackerEnergy	commit_considered_backbone_move (ObjexxFCL::FArray1_int &rotamer_on_node) override

PackerEnergy	project_deltaE_for_substitution (int alternate_state, PackerEnergy &prev_energy_for_node)
	Virtual functions from OTFFlexbbInteractionGraph. More...

Member Typedef Documentation

typedef OTFFlexbbInteractionGraph protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::parent

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::MinimalistFlexbbInteractionGraph ( int num_nodes )

GRAPH.

Referenced by count_static_memory().

protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::~MinimalistFlexbbInteractionGraph ( )

overridedefault

Member Function Documentation

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::blanket_assign_state_0 ( )

overridevirtual

State initialization.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::InteractionGraphBase.

References protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state(), get_minimalistflexbb_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_last_considered_substitution_resolved(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_node_considering_alt_state(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_current_state_assignment().

MinimalistFlexbbEdge const * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::cast_minimalist_flexbb_edge ( EdgeBase const * edge ) const

inlineprotected

References core::pack::interaction_graph::InteractionGraphBase::mine().

Referenced by get_edge_memory_usage(), and get_energy_sum_for_vertex_group().

MinimalistFlexbbEdge * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::cast_minimalist_flexbb_edge ( EdgeBase * edge )

inlineprotected

References core::pack::interaction_graph::InteractionGraphBase::mine().

MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move ( ObjexxFCL::FArray1_int & rotamer_on_node )

overrideprivatevirtual

Implements protocols::flexpack::interaction_graph::FlexbbInteractionGraph.

MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_substitution ( )

overridevirtual

Accept a considered substitution (i.e. make the substitution permanent; commit it).

Must be implemented by derived classes.

Implements core::pack::interaction_graph::InteractionGraphBase.

References protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_accepted_substitution(), get_minimalistflexbb_node(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::node_considering_alt_state(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_last_considered_substitution_resolved(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_current_state_assignment(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_alternate_state_assignment(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment().

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::complete_deltaE_prediction_for_bbmove	(	core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_energy_for_flexseg,
		bool &	valid_motion,
		int &	num_nodes_changing_state
	)

protected

References protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_considering_alt_bb(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members(), get_minimalistflexbb_node(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_nodes_changing_state(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_last_considered_backbone_sub_valid(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_alternate_state_assignment(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment().

Referenced by consider_backbone_move(), and consider_bbmove_w_state_substitution().

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move	(	int	bb_id,
		core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_flexseg_energy,
		bool &	valid_motion,
		int &	num_nodes_changing_state
	)

overridevirtual

Virtual functions from FlexbbInteractionGraph.

Implements protocols::flexpack::interaction_graph::FlexbbInteractionGraph.

References complete_deltaE_prediction_for_bbmove(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexbb_node(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_bb_offset(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_for_bb(), get_minimalistflexbb_node(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_unresolved(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_bbjump_substitution(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::reset_node_in_moving_flexseg_count(), resolve_uncommitted_substitution(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_flexseg_considering_alt_bb().

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_energy_for_flexseg,
		bool &	valid_motion,
		int &	num_nodes_changing_state
	)

overridevirtual

Implements protocols::flexpack::interaction_graph::FlexbbInteractionGraph.

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_substitution	(	int	node_ind,
		int	new_state,
		PackerEnergy &	delta_energy,
		PackerEnergy &	prev_energy_for_node
	)

overridevirtual

Consider switching node "node_ind" to state "new_state".

Must be implemented by derived classes.

Parameters

[in]	node_ind	The node index.
[in]	new_state	The state index that we are considering switching TO.
[out]	delta_energy	The change in energy that results from the switch under consideration, computed by this function.
[out]	prev_energy_for_node	The energy of this node prior to the substitutio, returned by this function.

Implements core::pack::interaction_graph::InteractionGraphBase.

References protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution(), get_minimalistflexbb_node(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_unresolved(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_fixedbb_substitution(), project_deltaE_for_substitution(), resolve_uncommitted_substitution(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_node_considering_alt_state(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_alternate_state_assignment(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment().

Referenced by consider_bbmove_w_state_substitution().

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

overrideprotectedvirtual

Reimplemented from protocols::flexpack::interaction_graph::FlexbbInteractionGraph.

References protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::count_dynamic_memory().

unsigned int protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::count_static_memory ( ) const

overrideprotectedvirtual

Virtual functions from InteractionGraphBase.

Implements core::pack::interaction_graph::InteractionGraphBase.

References MinimalistFlexbbInteractionGraph().

core::pack::interaction_graph::EdgeBase * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::create_new_edge	(	int	index1,
		int	index2
	)

overrideprotectedvirtual

Implements core::pack::interaction_graph::InteractionGraphBase.

core::pack::interaction_graph::NodeBase * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::create_new_node	(	int	node_index,
		int	num_states
	)

overrideprotectedvirtual

Implements core::pack::interaction_graph::InteractionGraphBase.

MinimalistFlexbbEdge const * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::find_minimalist_flexbb_edge	(	int	node1,
		int	node2
	)		const

inlineprotected

References core::pack::interaction_graph::InteractionGraphBase::find_edge().

MinimalistFlexbbEdge * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::find_minimalist_flexbb_edge	(	int	node1,
		int	node2
	)

inlineprotected

References core::pack::interaction_graph::InteractionGraphBase::find_edge().

int protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_edge_memory_usage ( ) const

overridevirtual

Implements core::pack::interaction_graph::InteractionGraphBase.

References cast_minimalist_flexbb_edge(), protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::count_dynamic_memory(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), and core::simple_metrics::metrics::sum.

MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_current_state_assignment ( )

overridevirtual

Get the energy resulting from the current set of state assignments.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::InteractionGraphBase.

References protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment().

MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_sum_for_vertex_group ( int group_id )

overridevirtual

Implements core::pack::interaction_graph::InteractionGraphBase.

References cast_minimalist_flexbb_edge(), protocols::flexpack::interaction_graph::FlexbbEdge::cur_energy(), protocols::flexpack::interaction_graph::FlexbbNode::curr_state_one_body_energy(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), get_minimalistflexbb_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), and core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group().

MinimalistFlexbbNode const * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_minimalistflexbb_node ( int index ) const

inlineprotected

Downcasts.

Graph Downcasts.

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

Referenced by blanket_assign_state_0(), commit_considered_backbone_move(), commit_considered_substitution(), complete_deltaE_prediction_for_bbmove(), consider_backbone_move(), consider_bbmove_w_state_substitution(), consider_substitution(), get_energy_sum_for_vertex_group(), get_one_body_energy_for_node_state(), print_current_state_assignment(), resolve_uncommitted_substitution(), set_network_state(), and set_state_for_node().

MinimalistFlexbbNode * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_minimalistflexbb_node ( int index )

inlineprotected

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

MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_one_body_energy_for_node_state	(	int	node,
		int	state
	)

overridevirtual

Implements core::pack::interaction_graph::InteractionGraphBase.

References get_minimalistflexbb_node(), and protocols::flexpack::interaction_graph::FlexbbNode::get_one_body_energy().

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::initialize ( core::pack_basic::RotamerSetsBase const & rot_sets )

overridevirtual

Virtual functions from InteractionGraphBase.

Reimplemented from protocols::flexpack::interaction_graph::FlexbbInteractionGraph.

References protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::initialize().

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::print_current_state_assignment ( ) const

overridevirtual

Implements core::pack::interaction_graph::InteractionGraphBase.

References protocols::flexpack::interaction_graph::FlexbbNode::get_current_state(), get_minimalistflexbb_node(), and core::pack::interaction_graph::InteractionGraphBase::get_num_nodes().

PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::project_deltaE_for_substitution	(	int	alternate_state,
		PackerEnergy &	prev_energy_for_node
	)

private

Virtual functions from OTFFlexbbInteractionGraph.

returns the change in energy that would be induced by switching this node from its current state into another state on the same backbone

Referenced by consider_substitution().

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::resolve_uncommitted_substitution ( )

protected

Referenced by consider_backbone_move(), consider_bbmove_w_state_substitution(), consider_substitution(), set_network_state(), and set_state_for_node().

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_errorfull_deltaE_threshold ( PackerEnergy deltaE )

overridevirtual

noop. This IG does not allow for inaccuracies in its energy function.

Implements core::pack::interaction_graph::InteractionGraphBase.

MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state ( ObjexxFCL::FArray1_int & node_states )

overridevirtual

Explicit state modification for the network.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::InteractionGraphBase.

MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node	(	int	node_ind,
		int	new_state
	)

overridevirtual

Explicit state modification for a node.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::InteractionGraphBase.

References protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_state(), get_minimalistflexbb_node(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_unresolved(), resolve_uncommitted_substitution(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_node_considering_alt_state(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_current_state_assignment(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::update_internal_energy_totals().

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

src/protocols/flexpack/interaction_graph/MinimalistFlexbbInteractionGraph.hh
src/protocols/flexpack/interaction_graph/MinimalistFlexbbInteractionGraph.cc

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