#include <MinimalistFlexbbInteractionGraph.hh>

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

Collaboration 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...

virtual	~MinimalistFlexbbInteractionGraph ()

virtual void	initialize (core::pack::rotamer_set::RotamerSetsBase const &rot_sets)
	Virtual functions from InteractionGraphBase. More...

virtual PackerEnergy	get_one_body_energy_for_node_state (int node, int state)

virtual void	blanket_assign_state_0 ()

virtual PackerEnergy	set_state_for_node (int node_ind, int new_state)

virtual PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states)

virtual void	consider_substitution (int node_ind, int new_state, PackerEnergy &delta_energy, PackerEnergy &prev_energy_for_node)

virtual PackerEnergy	commit_considered_substitution ()

virtual PackerEnergy	get_energy_current_state_assignment ()

virtual int	get_edge_memory_usage () const

virtual void	print_current_state_assignment () const

virtual void	set_errorfull_deltaE_threshold (PackerEnergy deltaE)

virtual PackerEnergy	get_energy_sum_for_vertex_group (int group_id)

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

virtual 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)

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

virtual	~OTFFlexbbInteractionGraph ()

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)

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
virtual	~FlexbbInteractionGraph ()
	GRAPH. More...

	FlexbbInteractionGraph (int num_nodes)

int	get_num_aa_types () const

utility::vector1< 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< Size > &rotlist) const

void	get_backbone_list (utility::vector1< 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
virtual	~InteractionGraphBase ()
	destructor More...

	InteractionGraphBase (int num_nodes)
	main constructor More...

virtual int	get_num_nodes_v () const

int	get_num_nodes () const

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
	returns the number of states for a particular node More...

int	get_num_total_states () const

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)
	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...

virtual void	prepare_for_simulated_annealing ()
	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
	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...

EdgeBase const *	find_edge (int node1, int node2) const
	returns the edge connecting node1 and node2 More...

EdgeBase *	find_edge (int node1, int node2)

NodeBase *	get_node (int index) const

int	get_num_edges () const

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

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

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

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)

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

virtual unsigned int	count_dynamic_memory () const

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

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

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	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
virtual PackerEnergy	commit_considered_backbone_move (ObjexxFCL::FArray1_int &rotamer_on_node)

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

Detailed Description

Definition at line 212 of file MinimalistFlexbbInteractionGraph.hh.

Member Typedef Documentation

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

Definition at line 215 of file MinimalistFlexbbInteractionGraph.hh.

Constructor & Destructor Documentation

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

GRAPH.

Definition at line 576 of file MinimalistFlexbbInteractionGraph.cc.

Referenced by count_static_memory().

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

virtual

Definition at line 580 of file MinimalistFlexbbInteractionGraph.cc.

Member Function Documentation

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

virtual

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

Definition at line 598 of file MinimalistFlexbbInteractionGraph.cc.

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

Definition at line 412 of file MinimalistFlexbbInteractionGraph.hh.

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

Definition at line 417 of file MinimalistFlexbbInteractionGraph.hh.

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

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

privatevirtual

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

Definition at line 915 of file MinimalistFlexbbInteractionGraph.cc.

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

virtual

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

Definition at line 680 of file MinimalistFlexbbInteractionGraph.cc.

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

Definition at line 873 of file MinimalistFlexbbInteractionGraph.cc.

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
	)

virtual

Virtual functions from FlexbbInteractionGraph.

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

Definition at line 755 of file MinimalistFlexbbInteractionGraph.cc.

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
	)

virtual

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

Definition at line 807 of file MinimalistFlexbbInteractionGraph.cc.

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

virtual

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

Definition at line 654 of file MinimalistFlexbbInteractionGraph.cc.

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

protectedvirtual

Reimplemented from protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph.

Definition at line 953 of file MinimalistFlexbbInteractionGraph.cc.

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

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

protectedvirtual

Virtual functions from InteractionGraphBase.

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

Definition at line 947 of file MinimalistFlexbbInteractionGraph.cc.

References MinimalistFlexbbInteractionGraph().

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

protectedvirtual

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

Definition at line 965 of file MinimalistFlexbbInteractionGraph.cc.

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

protectedvirtual

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

Definition at line 959 of file MinimalistFlexbbInteractionGraph.cc.

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

inlineprotected

Definition at line 394 of file MinimalistFlexbbInteractionGraph.hh.

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

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

inlineprotected

Definition at line 403 of file MinimalistFlexbbInteractionGraph.hh.

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

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

virtual

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

Definition at line 702 of file MinimalistFlexbbInteractionGraph.cc.

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

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

virtual

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

Definition at line 696 of file MinimalistFlexbbInteractionGraph.cc.

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)

virtual

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

Definition at line 731 of file MinimalistFlexbbInteractionGraph.cc.

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.

Definition at line 384 of file MinimalistFlexbbInteractionGraph.hh.

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

Definition at line 389 of file MinimalistFlexbbInteractionGraph.hh.

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
	)

virtual

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

Definition at line 589 of file MinimalistFlexbbInteractionGraph.cc.

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

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

virtual

Virtual functions from InteractionGraphBase.

Reimplemented from protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph.

Definition at line 583 of file MinimalistFlexbbInteractionGraph.cc.

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

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

virtual

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

Definition at line 714 of file MinimalistFlexbbInteractionGraph.cc.

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

Definition at line 972 of file MinimalistFlexbbInteractionGraph.cc.

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)

virtual

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

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

Definition at line 726 of file MinimalistFlexbbInteractionGraph.cc.

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

virtual

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

Definition at line 625 of file MinimalistFlexbbInteractionGraph.cc.

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

virtual

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

Definition at line 609 of file MinimalistFlexbbInteractionGraph.cc.

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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