#include <MinimalistFlexbbInteractionGraph.hh>

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...

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 ()

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...

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 ( )

virtual

Member Function Documentation

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

virtual

References protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state(), get_minimalistflexbb_node(), 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

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

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

privatevirtual

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

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

virtual

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
	)

virtual

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
	)

virtual

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
	)

virtual

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.

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.

References MinimalistFlexbbInteractionGraph().

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

protectedvirtual

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

protectedvirtual

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

inlineprotected

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

inlineprotected

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

virtual

References cast_minimalist_flexbb_edge(), protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::count_dynamic_memory(), and sum().

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

virtual

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

References cast_minimalist_flexbb_edge(), protocols::flexpack::interaction_graph::FlexbbEdge::cur_energy(), protocols::flexpack::interaction_graph::FlexbbNode::curr_state_one_body_energy(), and get_minimalistflexbb_node().

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

inlineprotected

Downcasts.

Graph Downcasts.

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

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

virtual

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.

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

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

virtual

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

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 )

virtual

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

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

virtual

References protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_accepted_substitution(), 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::MinimalistFlexbbNode::partially_assign_state(), resolve_uncommitted_substitution(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::update_internal_energy_totals().

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

virtual

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:

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

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 Types

Public Member Functions

Protected Member Functions

Private Member Functions

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation