#include <OTFFlexbbInteractionGraph.hh>

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

virtual	~OTFFlexbbInteractionGraph ()

virtual void	initialize (core::pack::rotamer_set::RotamerSetsBase const &)

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 unsigned int	count_dynamic_memory () const

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

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)=0

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)=0

virtual PackerEnergy	commit_considered_backbone_move (ObjexxFCL::FArray1_int &rotamer_on_node)=0

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
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 Attributes
PoseOP	pose_

ScoreFunctionOP	sfxn_

OtherContextScoreFunctionOP	oc_sfxn_

PoseOP	current_pose_
	For debugging purposes. More...

Real	current_pose_energy_

PoseOP	alternate_pose_

Real	alternate_pose_energy_

utility::vector1< Size >	changing_seqpos_

utility::vector1 < core::conformation::ResidueOP >	alt_rots_

utility::vector1< int >	alt_rot_inds_

utility::vector1< Size >	resid_2_moltenres_

utility::vector1< Size >	moltenres_2_resid_

Member Typedef Documentation

typedef FlexbbInteractionGraph protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::parent

typedef core::pose::Pose protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::Pose

typedef core::pose::PoseCOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::PoseCOP

typedef core::pose::PoseOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::PoseOP

typedef core::Real protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::Real

typedef core::scoring::ScoreFunction protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::ScoreFunction

typedef core::scoring::ScoreFunctionCOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::ScoreFunctionCOP

typedef core::scoring::ScoreFunctionOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::ScoreFunctionOP

Constructor & Destructor Documentation

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

GRAPH.

protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::~OTFFlexbbInteractionGraph ( )

virtual

Member Function Documentation

OTFFlexbbEdge const* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::cast_otfflexbb_edge ( EdgeBase const * edge ) const

inlineprotected

OTFFlexbbEdge* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::cast_otfflexbb_edge ( EdgeBase * edge )

inlineprotected

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

virtual

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

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph.

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

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

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_accepted_substitution ( )

References alt_rot_inds_, alt_rots_, alternate_pose_energy_, changing_seqpos_, current_pose_energy_, and utility_exit_with_message.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution	(	core::conformation::Residue const &	alt_rotamer,
		int	index
	)

References alt_rot_inds_, alt_rots_, alternate_pose_, changing_seqpos_, core::conformation::Residue::clone(), core::pose::Pose::replace_residue(), core::conformation::Residue::seqpos(), and utility_exit_with_message.

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().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution	(	PackerEnergy	deltaE,
		PackerEnergy	node_alt_total,
		bool	require_match = `true`
	)

References protocols::flexpack::interaction_graph::FlexbbEdge::alt_energy(), alt_rot_inds_, alternate_pose_, alternate_pose_energy_, protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_one_body_energy(), changing_seqpos_, current_pose_, current_pose_energy_, dot(), core::pose::Pose::dump_pdb(), core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), find_otfflexbb_edge(), core::pack::rotamer_set::RotamerSets::get_bb_bbE(), core::graph::Edge::get_node(), get_otfflexbb_node(), core::pack::rotamer_set::RotamerSets::get_sc_bbE(), oc_sfxn_, protocols::flexpack::interaction_graph::OTFFlexbbEdge::print_alt_energies(), resid_2_moltenres_, utility::to_string(), and utility_exit_with_message.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::complete_deltaE_prediction_for_bbmove(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_rejected_substitution ( )

References alt_rot_inds_, alt_rots_, changing_seqpos_, and utility_exit_with_message.

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

OTFFlexbbEdge const* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::find_otfflexbb_edge	(	int	node1,
		int	node2
	)		const

inlineprotected

Referenced by debug_note_projected_deltaE_of_considered_substitution(), note_long_range_interactions_exist_for_edge(), set_GlyCorrection_values_for_edge(), and set_ProCorrection_values_for_edge().

OTFFlexbbEdge* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::find_otfflexbb_edge	(	int	node1,
		int	node2
	)

inlineprotected

OTFFlexbbNode const* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_otfflexbb_node ( int index ) const

inlineprotected

Downcasts.

Referenced by debug_note_projected_deltaE_of_considered_substitution(), and initialize().

OTFFlexbbNode* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_otfflexbb_node ( int index )

inlineprotected

OTFFlexbbInteractionGraph::PoseCOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_pose ( ) const

Edges request the pose and the score function at the time of their creation.

References pose_.

OTFFlexbbInteractionGraph::ScoreFunctionCOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_scorefxn ( ) const

References sfxn_.

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

virtual

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

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph.

References protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), get_otfflexbb_node(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), moltenres_2_resid_, resid_2_moltenres_, and protocols::flexpack::interaction_graph::OTFFlexbbNode::set_rotamer().

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

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::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.

References find_otfflexbb_edge(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::note_long_range_interactions_exist().

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::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
	)

References find_otfflexbb_edge(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_GlyCorrection_values().

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_pose ( Pose const & pose )

virtual

Pose must be set before any edges are added to the graph.

References alternate_pose_, current_pose_, moltenres_2_resid_, pose_, resid_2_moltenres_, and core::pose::Pose::total_residue().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::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
	)

References find_otfflexbb_edge(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_ProCorrection_values().

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_scorefxn ( ScoreFunction const & sfxn )

virtual

Score function must be set before any edges are added to the graph.

References core::scoring::ScoreFunction::clone(), n_score_types, oc_sfxn_, pose_, and sfxn_.

Member Data Documentation

utility::vector1< int > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::alt_rot_inds_

private

Referenced by debug_note_accepted_substitution(), debug_note_considered_substitution(), debug_note_projected_deltaE_of_considered_substitution(), and debug_note_rejected_substitution().

utility::vector1< core::conformation::ResidueOP > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::alt_rots_

private

Referenced by debug_note_accepted_substitution(), debug_note_considered_substitution(), and debug_note_rejected_substitution().

PoseOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::alternate_pose_

private

Referenced by debug_note_considered_substitution(), debug_note_projected_deltaE_of_considered_substitution(), and set_pose().

Real protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::alternate_pose_energy_

private

Referenced by debug_note_accepted_substitution(), and debug_note_projected_deltaE_of_considered_substitution().

utility::vector1< Size > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::changing_seqpos_

private

Referenced by debug_note_accepted_substitution(), debug_note_considered_substitution(), debug_note_projected_deltaE_of_considered_substitution(), and debug_note_rejected_substitution().

PoseOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::current_pose_

private

For debugging purposes.

Referenced by debug_note_projected_deltaE_of_considered_substitution(), and set_pose().

Real protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::current_pose_energy_

private

Referenced by debug_note_accepted_substitution(), and debug_note_projected_deltaE_of_considered_substitution().

utility::vector1< Size > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::moltenres_2_resid_

private

Referenced by initialize(), and set_pose().

OtherContextScoreFunctionOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::oc_sfxn_

private

Referenced by debug_note_projected_deltaE_of_considered_substitution(), and set_scorefxn().

PoseOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::pose_

private

Referenced by get_pose(), set_pose(), and set_scorefxn().

utility::vector1< Size > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::resid_2_moltenres_

private

Referenced by debug_note_projected_deltaE_of_considered_substitution(), initialize(), and set_pose().

ScoreFunctionOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::sfxn_

private

Referenced by get_scorefxn(), and set_scorefxn().

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

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

Public Types
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 Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation