protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph Class Reference

#include <OTFFlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph:

Collaboration diagram for protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph:

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 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...
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
virtual core::PackerEnergy	get_one_body_energy_for_node_state (int node, int state)=0
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...
virtual void	blanket_assign_state_0 ()=0
virtual core::PackerEnergy	set_state_for_node (int node_ind, int new_state)=0
virtual core::PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states)=0
virtual void	consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node)=0
virtual core::PackerEnergy	commit_considered_substitution ()=0
virtual core::PackerEnergy	get_energy_current_state_assignment ()=0
void	set_edge_weight (int node1, int node2, Real edge_weight)
Real	get_edge_weight (int node1, int node2) const
virtual int	get_edge_memory_usage () const =0
virtual void	print_current_state_assignment () const =0
virtual void	set_errorfull_deltaE_threshold (core::PackerEnergy deltaE)=0
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 ()
virtual core::PackerEnergy	get_energy_sum_for_vertex_group (int group_id)=0
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)
virtual NodeBase *	create_new_node (int node_index, int num_states)=0
virtual EdgeBase *	create_new_edge (int index1, int index2)=0
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
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
virtual unsigned int	count_static_memory () const =0
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 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_

Detailed Description

Definition at line 240 of file OTFFlexbbInteractionGraph.hh.

Member Typedef Documentation

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

Definition at line 243 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 247 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 246 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 245 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 244 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 250 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 249 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 248 of file OTFFlexbbInteractionGraph.hh.

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::OTFFlexbbInteractionGraph

(

int

num_nodes)

GRAPH.

Definition at line 662 of file OTFFlexbbInteractionGraph.cc.

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

virtual

Definition at line 668 of file OTFFlexbbInteractionGraph.cc.

Member Function Documentation

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

inlineprotected

Definition at line 328 of file OTFFlexbbInteractionGraph.hh.

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

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

inlineprotected

Definition at line 331 of file OTFFlexbbInteractionGraph.hh.

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

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.

Definition at line 736 of file OTFFlexbbInteractionGraph.cc.

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

(

)

Definition at line 1023 of file OTFFlexbbInteractionGraph.cc.

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

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
	)

Definition at line 817 of file OTFFlexbbInteractionGraph.cc.

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

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
	)

Definition at line 831 of file OTFFlexbbInteractionGraph.cc.

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(), core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned(), changing_seqpos_, current_pose_, current_pose_energy_, 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(), and resid_2_moltenres_.

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

(

)

Definition at line 1037 of file OTFFlexbbInteractionGraph.cc.

References alt_rot_inds_, alt_rots_, and changing_seqpos_.

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

Definition at line 314 of file OTFFlexbbInteractionGraph.hh.

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

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

Definition at line 321 of file OTFFlexbbInteractionGraph.hh.

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

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

inlineprotected

Downcasts.

Definition at line 308 of file OTFFlexbbInteractionGraph.hh.

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

Referenced by debug_note_projected_deltaE_of_considered_substitution(), and initialize().

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

inlineprotected

Definition at line 311 of file OTFFlexbbInteractionGraph.hh.

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

OTFFlexbbInteractionGraph::PoseCOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_pose

(

)

const

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

Definition at line 789 of file OTFFlexbbInteractionGraph.cc.

References pose_.

OTFFlexbbInteractionGraph::ScoreFunctionCOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_scorefxn

(

)

const

Definition at line 796 of file OTFFlexbbInteractionGraph.cc.

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.

Definition at line 672 of file OTFFlexbbInteractionGraph.cc.

References protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_otfflexbb_node(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), core::pack::rotamer_set::RotamerSetsBase::moltenres_2_resid(), moltenres_2_resid_, core::pack::rotamer_set::RotamerSetsBase::nmoltenres(), core::pack::rotamer_set::RotamerSetsBase::nrotamer_offset_for_moltenres(), core::pack::rotamer_set::RotamerSetsBase::nrotamers_for_moltenres(), resid_2_moltenres_, core::pack::rotamer_set::RotamerSetsBase::rotamer(), 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.

Definition at line 803 of file OTFFlexbbInteractionGraph.cc.

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
	)

Definition at line 717 of file OTFFlexbbInteractionGraph.cc.

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.

Definition at line 743 of file OTFFlexbbInteractionGraph.cc.

References alternate_pose_, current_pose_, core::pack::interaction_graph::InteractionGraphBase::get_num_edges(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), 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
	)

Definition at line 699 of file OTFFlexbbInteractionGraph.cc.

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.

Definition at line 759 of file OTFFlexbbInteractionGraph.cc.

References core::pack::interaction_graph::InteractionGraphBase::get_num_edges(), core::scoring::n_score_types, oc_sfxn_, pose_, sfxn_, and core::scoring::ScoreFunction::weights().

Member Data Documentation

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

private

Definition at line 349 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 348 of file OTFFlexbbInteractionGraph.hh.

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

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

private

Definition at line 344 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 345 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 347 of file OTFFlexbbInteractionGraph.hh.

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.

Definition at line 342 of file OTFFlexbbInteractionGraph.hh.

Referenced by debug_note_projected_deltaE_of_considered_substitution(), and set_pose().

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

private

Definition at line 343 of file OTFFlexbbInteractionGraph.hh.

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

Definition at line 352 of file OTFFlexbbInteractionGraph.hh.

Referenced by initialize(), and set_pose().

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

private

Definition at line 339 of file OTFFlexbbInteractionGraph.hh.

Referenced by debug_note_projected_deltaE_of_considered_substitution(), and set_scorefxn().

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

private

Definition at line 337 of file OTFFlexbbInteractionGraph.hh.

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

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

private

Definition at line 351 of file OTFFlexbbInteractionGraph.hh.

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

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

private

Definition at line 338 of file OTFFlexbbInteractionGraph.hh.

Referenced by get_scorefxn(), and set_scorefxn().

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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