protocols::flexpack::interaction_graph::FlexbbInteractionGraph Class Reference

#include <FlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::FlexbbInteractionGraph:

Collaboration diagram for protocols::flexpack::interaction_graph::FlexbbInteractionGraph:

Public Types
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
virtual	~FlexbbInteractionGraph ()
	GRAPH. More...
	FlexbbInteractionGraph (int num_nodes)
virtual void	initialize (core::pack::rotamer_set::RotamerSetsBase const &rot_sets)
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...
virtual unsigned int	count_dynamic_memory () const
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
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 Member Functions
void	set_num_flexsegs (int num_flexsegs)
	Private functions called during initialize() More...
void	set_total_num_backbones (int num_backbones)
void	set_num_bb_for_node (int node, int numbb)
void	set_num_states_per_backbone_for_node (int node, utility::vector1< int > const &states_per_bb)
void	set_aatypes_for_node (int node_ind, utility::vector1< int > const &aatypes)
void	set_closest_states_on_other_bbs (int node_index, ObjexxFCL::FArray2D_int const &)
	FlexbbInteractionGraph ()
	FlexbbInteractionGraph (FlexbbInteractionGraph const &)

Private Attributes
int	num_aa_types_
PackerEnergy	total_energy_current_state_assignment_
PackerEnergy	total_energy_alternate_state_assignment_
int	node_considering_alt_state_
int	flexseg_considering_alt_bb_
int	num_flexible_segments_
int	num_total_bb_
utility::vector1 < utility::vector1< Size > >	flexseg_members_
utility::vector1< int >	num_bb_alternatives_for_flexseg_
utility::vector1< int >	flexseg_for_bb_
utility::vector1< int >	flexseg_bb_offset_
utility::vector1< int >	flexseg_for_moltenres_
bool	enforce_bb_contiguity_
bool	last_sub_attempted_backbone_move_
bool	last_considered_backbone_sub_valid_
bool	last_considered_backbone_sub_unresolved_
bool	last_considered_fixedbb_sub_unresolved_
int	num_nodes_changing_state_
int	num_commits_since_last_update_

Static Private Attributes
static const int	COMMIT_LIMIT_BETWEEN_UPDATES = 20

Detailed Description

Definition at line 432 of file FlexbbInteractionGraph.hh.

Member Typedef Documentation

typedef core::pack::interaction_graph::EdgeBase protocols::flexpack::interaction_graph::FlexbbInteractionGraph::EdgeBase

Definition at line 437 of file FlexbbInteractionGraph.hh.

typedef core::PackerEnergy protocols::flexpack::interaction_graph::FlexbbInteractionGraph::PackerEnergy

Definition at line 436 of file FlexbbInteractionGraph.hh.

typedef core::pack::interaction_graph::InteractionGraphBase protocols::flexpack::interaction_graph::FlexbbInteractionGraph::parent

Definition at line 435 of file FlexbbInteractionGraph.hh.

Member Enumeration Documentation

enum protocols::flexpack::interaction_graph::FlexbbInteractionGraph::Subsitution

Enumerator
SC_ONLY
BOTH_SC_AND_BB

Definition at line 440 of file FlexbbInteractionGraph.hh.

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::FlexbbInteractionGraph::~FlexbbInteractionGraph ( )

virtual

GRAPH.

Definition at line 579 of file FlexbbInteractionGraph.cc.

protocols::flexpack::interaction_graph::FlexbbInteractionGraph::FlexbbInteractionGraph

(

int

num_nodes)

Definition at line 580 of file FlexbbInteractionGraph.cc.

protocols::flexpack::interaction_graph::FlexbbInteractionGraph::FlexbbInteractionGraph ( )

private

protocols::flexpack::interaction_graph::FlexbbInteractionGraph::FlexbbInteractionGraph ( FlexbbInteractionGraph const &  )

private

Member Function Documentation

FlexbbEdge const* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::cast_flexbb_edge ( EdgeBase const *  edge) const

inlineprotected

Definition at line 553 of file FlexbbInteractionGraph.hh.

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

Referenced by update_internal_energy_totals().

FlexbbEdge* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::cast_flexbb_edge ( EdgeBase *  edge)

inlineprotected

Definition at line 556 of file FlexbbInteractionGraph.hh.

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

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

pure virtual

Implemented in protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph.

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

pure virtual

Implemented in protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph.

virtual void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::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  )

pure virtual

Implemented in protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph.

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

virtual

Reimplemented from core::pack::interaction_graph::InteractionGraphBase.

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph, and protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph.

Definition at line 896 of file FlexbbInteractionGraph.cc.

References core::pack::interaction_graph::InteractionGraphBase::count_dynamic_memory(), flexseg_bb_offset_, flexseg_for_bb_, flexseg_members_, and num_bb_alternatives_for_flexseg_.

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

FlexbbEdge const* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::find_flexbb_edge ( int  node1, int  node2  ) const

inlineprotected

Definition at line 539 of file FlexbbInteractionGraph.hh.

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

FlexbbEdge* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::find_flexbb_edge ( int  node1, int  node2  )

inlineprotected

Definition at line 546 of file FlexbbInteractionGraph.hh.

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

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_considering_alt_bb ( ) const

inlineprotected

Only allowed to ask for the flexible segment considering an alternate backbone conformation during a backbone-moving substitution.

Definition at line 589 of file FlexbbInteractionGraph.hh.

References flexseg_considering_alt_bb_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::complete_deltaE_prediction_for_bbmove(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::resolve_uncommitted_substitution().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_for_moltenres ( int  moltenres) const

inlineprotected

Definition at line 593 of file FlexbbInteractionGraph.hh.

References flexseg_for_moltenres_.

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

utility::vector1< Size > const& protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members ( int  flexseg) const

inline

Definition at line 458 of file FlexbbInteractionGraph.hh.

References flexseg_members_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::complete_deltaE_prediction_for_bbmove(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::resolve_uncommitted_substitution().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states	(	Subsitution	move_mode,
		utility::vector1< Size > &	rotlist
	)		const

Definition at line 841 of file FlexbbInteractionGraph.cc.

References protocols::flexpack::interaction_graph::FlexbbNode::get_all_states(), get_flexbb_node(), core::pack::interaction_graph::InteractionGraphBase::get_node_state_offset(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), protocols::flexpack::interaction_graph::FlexbbNode::get_states_on_curr_bb(), and SC_ONLY.

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::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.

Definition at line 871 of file FlexbbInteractionGraph.cc.

References flexseg_for_bb_, flexseg_members_, protocols::flexpack::interaction_graph::FlexbbNode::get_backbone_for_current_state(), and get_flexbb_node().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_list

(

utility::vector1< Size > &

bblist)

const

Definition at line 857 of file FlexbbInteractionGraph.cc.

References num_total_bb_.

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_bb_for_state	(	int	node,
		int	state
	)		const

Definition at line 800 of file FlexbbInteractionGraph.cc.

References protocols::flexpack::interaction_graph::FlexbbNode::get_bb_for_state(), and get_flexbb_node().

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::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.

Definition at line 883 of file FlexbbInteractionGraph.cc.

References enforce_bb_contiguity_.

FlexbbNode const* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexbb_node ( int  index) const

inlineprotected

Downcasts.

Definition at line 533 of file FlexbbInteractionGraph.hh.

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

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution(), get_accessible_states(), get_backbone_currently_assigned(), get_bb_for_state(), get_num_states_per_backbone_for_node(), initialize(), set_aatypes_for_node(), set_closest_states_on_other_bbs(), set_num_bb_for_node(), set_num_states_per_backbone_for_node(), and update_internal_energy_totals().

FlexbbNode* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexbb_node ( int  index)

inlineprotected

Definition at line 536 of file FlexbbInteractionGraph.hh.

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

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_bb_offset ( int  flexseg_id) const

inline

Definition at line 462 of file FlexbbInteractionGraph.hh.

References flexseg_bb_offset_.

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

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_for_bb ( int  bb) const

inline

Definition at line 461 of file FlexbbInteractionGraph.hh.

References flexseg_for_bb_.

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

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_aa_types ( ) const

inline

Definition at line 454 of file FlexbbInteractionGraph.hh.

References num_aa_types_.

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_nodes_changing_state ( ) const

protected

Definition at line 944 of file FlexbbInteractionGraph.cc.

References num_nodes_changing_state_.

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

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_states_per_backbone_for_node	(	int	node,
		int	bb
	)		const

Definition at line 794 of file FlexbbInteractionGraph.cc.

References get_flexbb_node(), and protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_bb().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::increment_count_nodes_in_flexseg

(

)

Owner keeps a count of the number of nodes undergoing a simultaneous rotamer substitution as the backbone moves.

I don't remember what this is for... prev: increment_count_nodes_in_moving_fragment.

Definition at line 890 of file FlexbbInteractionGraph.cc.

References num_nodes_changing_state_.

Referenced by protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump().

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

virtual

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

Reimplemented in protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph, and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph.

Definition at line 599 of file FlexbbInteractionGraph.cc.

References flexseg_bb_offset_, flexseg_for_bb_, flexseg_for_moltenres_, flexseg_members_, protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegid_for_moltenres(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_start_moltenresid(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_stop_moltenresid(), get_flexbb_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_bb(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::local_rotid_start_for_moltenres_in_bbconf(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbackbone_conformations(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_moltenres(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nflexible_segments(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nmoltenres(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_moltenres(), num_aa_types_, num_bb_alternatives_for_flexseg_, num_flexible_segments_, protocols::flexpack::rotamer_set::FlexbbRotamerSets::num_states_per_backbone_for_moltenres(), num_total_bb_, protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotset_for_moltenres(), set_aatypes_for_node(), protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs(), protocols::flexpack::interaction_graph::FlexbbNode::set_num_distinct_backbones(), set_num_flexsegs(), core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node(), protocols::flexpack::interaction_graph::FlexbbNode::set_num_states_per_backbone(), set_total_num_backbones(), and core::conformation::Residue::xyz().

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

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_backbone_sub_unresolved ( ) const

inlineprotected

Definition at line 568 of file FlexbbInteractionGraph.hh.

References last_considered_backbone_sub_unresolved_.

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_backbone_sub_valid ( ) const

inlineprotected

Definition at line 591 of file FlexbbInteractionGraph.hh.

References last_considered_backbone_sub_valid_.

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

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_kept_backbone_fixed ( ) const

inlineprotected

Definition at line 565 of file FlexbbInteractionGraph.hh.

References last_sub_attempted_backbone_move_.

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

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_moved_the_backbone ( ) const

inlineprotected

Definition at line 566 of file FlexbbInteractionGraph.hh.

References last_sub_attempted_backbone_move_.

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

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_unresolved ( ) const

inlineprotected

Definition at line 569 of file FlexbbInteractionGraph.hh.

References last_considered_backbone_sub_unresolved_, and last_considered_fixedbb_sub_unresolved_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::resolve_uncommitted_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::node_considering_alt_state ( ) const

inlineprotected

Only allowed to ask for the node considering an alternate state during a fixed-backbone substitution.

Definition at line 585 of file FlexbbInteractionGraph.hh.

References node_considering_alt_state_.

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::resolve_uncommitted_substitution().

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::nodes_from_same_flexseg	(	int	node1,
		int	node2
	)		const

Definition at line 765 of file FlexbbInteractionGraph.cc.

References flexseg_for_moltenres_.

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_bbjump_substitution ( )

inlineprotected

Definition at line 563 of file FlexbbInteractionGraph.hh.

References last_sub_attempted_backbone_move_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_fixedbb_substitution ( )

inlineprotected

Definition at line 564 of file FlexbbInteractionGraph.hh.

References last_considered_fixedbb_sub_unresolved_, and last_sub_attempted_backbone_move_.

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

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_last_considered_substitution_resolved ( )

protected

Definition at line 929 of file FlexbbInteractionGraph.cc.

References last_considered_backbone_sub_unresolved_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::blanket_assign_state_0(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::resolve_uncommitted_substitution().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::reset_node_in_moving_flexseg_count ( )

protected

at the beginning of backbone-changing substitutions, derived classes must invoke this function to get a proper count of the number of nodes undergoing a simultaneous rotamer substitution

Definition at line 935 of file FlexbbInteractionGraph.cc.

References num_nodes_changing_state_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_aatypes_for_node ( int  node_ind, utility::vector1< int > const &  aatypes  )

private

Definition at line 806 of file FlexbbInteractionGraph.cc.

References get_flexbb_node(), and protocols::flexpack::interaction_graph::FlexbbNode::set_amino_acid_types().

Referenced by initialize().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_closest_states_on_other_bbs ( int  node_index, ObjexxFCL::FArray2D_int const &    )

private

Definition at line 815 of file FlexbbInteractionGraph.cc.

References get_flexbb_node(), and protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_enforce_bb_contiguity ( bool  setting)

protected

Definition at line 922 of file FlexbbInteractionGraph.cc.

References enforce_bb_contiguity_.

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_flexseg_considering_alt_bb ( int  setting)

inlineprotected

Track the last flexible segment at which a moving-backbone substitution took place.

Definition at line 606 of file FlexbbInteractionGraph.hh.

References flexseg_considering_alt_bb_, and node_considering_alt_state_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_last_considered_backbone_sub_valid ( bool  setting)

inlineprotected

Definition at line 610 of file FlexbbInteractionGraph.hh.

References last_considered_backbone_sub_valid_.

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

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_node_considering_alt_state ( int  setting)

inlineprotected

Track the last node at which a fixed-backbone substitution took place.

Definition at line 601 of file FlexbbInteractionGraph.hh.

References flexseg_considering_alt_bb_, and node_considering_alt_state_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::blanket_assign_state_0(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_num_bb_for_node ( int  node, int  numbb  )

private

Only call once. – depricated!

Must include initial backbone as well all the alternative backbones.

Definition at line 780 of file FlexbbInteractionGraph.cc.

References get_flexbb_node(), and protocols::flexpack::interaction_graph::FlexbbNode::set_num_distinct_backbones().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_num_flexsegs ( int  num_flexsegs)

private

Private functions called during initialize()

Definition at line 740 of file FlexbbInteractionGraph.cc.

References flexseg_bb_offset_, flexseg_members_, num_bb_alternatives_for_flexseg_, and num_flexible_segments_.

Referenced by initialize().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_num_states_per_backbone_for_node ( int  node, utility::vector1< int > const &  states_per_bb  )

private

Definition at line 786 of file FlexbbInteractionGraph.cc.

References get_flexbb_node(), and protocols::flexpack::interaction_graph::FlexbbNode::set_num_states_per_backbone().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_alternate_state_assignment ( PackerEnergy  setting)

inlineprotected

Definition at line 598 of file FlexbbInteractionGraph.hh.

References total_energy_alternate_state_assignment_.

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

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_current_state_assignment ( PackerEnergy  setting)

protected

Definition at line 911 of file FlexbbInteractionGraph.cc.

References COMMIT_LIMIT_BETWEEN_UPDATES, num_commits_since_last_update_, total_energy_current_state_assignment_, and update_internal_energy_totals().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::blanket_assign_state_0(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_num_backbones ( int  num_backbones)

private

Definition at line 754 of file FlexbbInteractionGraph.cc.

References flexseg_bb_offset_, flexseg_for_bb_, and num_total_bb_.

Referenced by initialize().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_alternate_state_assignment ( ) const

inlineprotected

Definition at line 581 of file FlexbbInteractionGraph.hh.

References total_energy_alternate_state_assignment_.

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

PackerEnergy protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment ( ) const

inlineprotected

Definition at line 580 of file FlexbbInteractionGraph.hh.

References total_energy_current_state_assignment_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::complete_deltaE_prediction_for_bbmove(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_substitution(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_current_state_assignment(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::update_internal_energy_totals ( )

protectedvirtual

Definition at line 949 of file FlexbbInteractionGraph.cc.

References cast_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_flexbb_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), num_commits_since_last_update_, total_energy_current_state_assignment_, and protocols::flexpack::interaction_graph::FlexbbNode::update_internal_energy_sums().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node(), and set_total_energy_current_state_assignment().

Member Data Documentation

const int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::COMMIT_LIMIT_BETWEEN_UPDATES = 20

staticprivate

Definition at line 642 of file FlexbbInteractionGraph.hh.

Referenced by set_total_energy_current_state_assignment().

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::enforce_bb_contiguity_

private

Definition at line 633 of file FlexbbInteractionGraph.hh.

Referenced by get_enforce_bb_contiguity(), and set_enforce_bb_contiguity().

utility::vector1< int > protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_bb_offset_

private

Definition at line 630 of file FlexbbInteractionGraph.hh.

Referenced by count_dynamic_memory(), get_flexseg_bb_offset(), initialize(), set_num_flexsegs(), and set_total_num_backbones().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_considering_alt_bb_

private

Definition at line 622 of file FlexbbInteractionGraph.hh.

Referenced by flexseg_considering_alt_bb(), set_flexseg_considering_alt_bb(), and set_node_considering_alt_state().

utility::vector1< int > protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_for_bb_

private

Definition at line 629 of file FlexbbInteractionGraph.hh.

Referenced by count_dynamic_memory(), get_backbone_currently_assigned(), get_flexseg_for_bb(), initialize(), and set_total_num_backbones().

utility::vector1< int > protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_for_moltenres_

private

Definition at line 631 of file FlexbbInteractionGraph.hh.

Referenced by flexseg_for_moltenres(), initialize(), and nodes_from_same_flexseg().

utility::vector1< utility::vector1< Size > > protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members_

private

Definition at line 627 of file FlexbbInteractionGraph.hh.

Referenced by count_dynamic_memory(), flexseg_members(), get_backbone_currently_assigned(), initialize(), and set_num_flexsegs().

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_backbone_sub_unresolved_

private

Definition at line 636 of file FlexbbInteractionGraph.hh.

Referenced by last_considered_backbone_sub_unresolved(), last_considered_substitution_unresolved(), and note_last_considered_substitution_resolved().

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_backbone_sub_valid_

private

Definition at line 635 of file FlexbbInteractionGraph.hh.

Referenced by last_considered_backbone_sub_valid(), and set_last_considered_backbone_sub_valid().

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_fixedbb_sub_unresolved_

private

Definition at line 637 of file FlexbbInteractionGraph.hh.

Referenced by last_considered_substitution_unresolved(), and note_fixedbb_substitution().

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_sub_attempted_backbone_move_

private

Definition at line 634 of file FlexbbInteractionGraph.hh.

Referenced by last_considered_substitution_kept_backbone_fixed(), last_considered_substitution_moved_the_backbone(), note_bbjump_substitution(), and note_fixedbb_substitution().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::node_considering_alt_state_

private

Definition at line 621 of file FlexbbInteractionGraph.hh.

Referenced by node_considering_alt_state(), set_flexseg_considering_alt_bb(), and set_node_considering_alt_state().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::num_aa_types_

private

Definition at line 617 of file FlexbbInteractionGraph.hh.

Referenced by get_num_aa_types(), and initialize().

utility::vector1< int > protocols::flexpack::interaction_graph::FlexbbInteractionGraph::num_bb_alternatives_for_flexseg_

private

Definition at line 628 of file FlexbbInteractionGraph.hh.

Referenced by count_dynamic_memory(), initialize(), and set_num_flexsegs().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::num_commits_since_last_update_

private

Definition at line 641 of file FlexbbInteractionGraph.hh.

Referenced by set_total_energy_current_state_assignment(), and update_internal_energy_totals().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::num_flexible_segments_

private

Definition at line 624 of file FlexbbInteractionGraph.hh.

Referenced by initialize(), and set_num_flexsegs().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::num_nodes_changing_state_

private

Definition at line 638 of file FlexbbInteractionGraph.hh.

Referenced by get_num_nodes_changing_state(), increment_count_nodes_in_flexseg(), and reset_node_in_moving_flexseg_count().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::num_total_bb_

private

Definition at line 625 of file FlexbbInteractionGraph.hh.

Referenced by get_backbone_list(), initialize(), and set_total_num_backbones().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_alternate_state_assignment_

private

Definition at line 620 of file FlexbbInteractionGraph.hh.

Referenced by set_total_energy_alternate_state_assignment(), and total_energy_alternate_state_assignment().

PackerEnergy protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment_

private

Definition at line 619 of file FlexbbInteractionGraph.hh.

Referenced by set_total_energy_current_state_assignment(), total_energy_current_state_assignment(), and update_internal_energy_totals().

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

• src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.hh
• src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.cc