#include <InteractionGraphBase.hh>

Inheritance diagram for core::pack::interaction_graph::InteractionGraphBase:

Public Member Functions
	~InteractionGraphBase () override
	destructor More...

	InteractionGraphBase (int num_nodes)
	main constructor More...

int	get_num_nodes () const override
	Get the number of nodes in the graph. More...

virtual void	initialize (pack_basic::RotamerSetsBase const &rot_sets)=0

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

int	get_num_total_states () const override
	Get the total number of states. More...

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) const
	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...

void	set_onebody_energies_multithreaded (core::Size const node_index, core::pack::rotamer_set::RotamerSetCOP rotset, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_assignments)
	Compute and store the onebody energy for all rotamers at a position. Safe for a multithreaded context. More...

void	prepare_graph_for_simulated_annealing () override
	iterate across edges and nodes and allow them to prepare for simulated annealing More...

void	blanket_assign_state_0 () override=0
	State initialization. More...

core::PackerEnergy	set_state_for_node (int node_ind, int new_state) override=0
	Explicit state modification for a node. More...

core::PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states) override=0
	Explicit state modification for the network. More...

void	consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override=0
	Consider switching node "node_ind" to state "new_state". More...

core::PackerEnergy	commit_considered_substitution () override=0
	Accept a considered substitution (i.e. make the substitution permanent; commit it). More...

core::PackerEnergy	get_energy_current_state_assignment () override=0
	Get the energy resulting from the current set of state assignments. More...

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

void	set_errorfull_deltaE_threshold (core::PackerEnergy deltaE) override=0
	Set an error threshold. More...

bool	any_vertex_state_unassigned () const override
	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...

virtual void	declare_all_edge_energies_final ()
	Iterates over all edges and calls declare_energies_final() on all of them. Takes O(N) time, where N is the number of edges. More...

EdgeBase const *	find_edge (int node1, int node2, bool const use_threadsafe_lookup=false) const
	Find an edge and return a const pointer to it. More...

EdgeBase *	find_edge (int node1, int node2, bool const use_threadsafe_lookup=false)
	Find an edge and return a nonconst pointer to it. More...

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 * >::iterator	get_edge_list_end ()

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

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

Public Member Functions inherited from core::pack::interaction_graph::AnnealableGraphBase
	AnnealableGraphBase ()
	Constructor. More...

	AnnealableGraphBase (AnnealableGraphBase const &src)
	Copy constructor. More...

	~AnnealableGraphBase () override
	Destructor. More...

virtual void	clean_up_after_packing (core::pose::Pose &pose)
	Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing. More...

Protected Member Functions
void	clean_up_edges_marked_for_deletion ()
	Remove those edges that have marked themselves for deletion. More...

virtual unsigned int	count_static_memory () const =0

virtual unsigned int	count_dynamic_memory () const

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
	InteractionGraphBase ()

	InteractionGraphBase (InteractionGraphBase const &)

InteractionGraphBase &	operator= (InteractionGraphBase const &)

Private Attributes
int	num_ig_nodes_

std::vector< NodeBase * >	ig_nodes_

std::list< EdgeBase * >	ig_edge_list_

std::vector< int >	node_state_offsets_

int	num_total_states_

EdgeBase *	focused_edge_

std::list< EdgeBase * > ::const_iterator	focused_edge_iterator_

std::list< EdgeBase * > ::const_iterator	focused_edge_iterator_end_

int	num_energy_sum_groups_

ObjexxFCL::FArray2D_bool	energy_sum_group_membership_

ObjexxFCL::FArray1D_int	component_membership_

Friends
class	NodeBase

class	EdgeBase

Constructor & Destructor Documentation

core::pack::interaction_graph::InteractionGraphBase::~InteractionGraphBase ( )

override

destructor

deletes each edge in the graph and deletes each node

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References ig_edge_list_, ig_nodes_, and num_ig_nodes_.

core::pack::interaction_graph::InteractionGraphBase::InteractionGraphBase ( int num_ig_nodes )

main constructor

no default or copy constructors provided.

Parameters

num_ig_nodes - [in] - number of nodes that this graph will contain

Global Read:

Global Write:

Remarks

References:

Author: apl

core::pack::interaction_graph::InteractionGraphBase::InteractionGraphBase ( )

private

core::pack::interaction_graph::InteractionGraphBase::InteractionGraphBase ( InteractionGraphBase const & )

private

Member Function Documentation

void core::pack::interaction_graph::InteractionGraphBase::add_edge	(	int	index1,
		int	index2
	)

creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order

uses factory method create_new_edge and adds the created edge to the graph's edge list.

Parameters

index1	- [in] - index of one of the two nodes the edge is to connect
index2	- [in] - index of the second of the two nodes the edge is to connect

Global Read:

Global Write:

Remarks

References:

Author: apl

References create_new_edge(), focused_edge_, ig_edge_list_, and core::pack::interaction_graph::EdgeBase::set_pos_in_owners_list().

Referenced by core::pack::interaction_graph::PDInteractionGraph::add_edge(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig(), and protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets().

void core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy	(	int	node_ind,
		utility::vector1< core::PackerEnergy > const &	one_body_energies
	)

Parameters

node_ind	- [in] - the node in question
one_body_energies	- [in] - the energies to be added to the one-body energies on that node. One entry per state.

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_onebody_interactions_with_background(), and set_onebody_energies_multithreaded().

void core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy	(	int	node_ind,
		ObjexxFCL::FArray1< core::PackerEnergy > const &	one_body_energies
	)

void core::pack::interaction_graph::InteractionGraphBase::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

Parameters

node_ind	- [in] - the index of the node in question
state_id	- [in] - the state in question
one_body_energy	- [in] - the energy to be added

void core::pack::interaction_graph::InteractionGraphBase::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

The input array should have {v} |S_v| entries, where S_v is the state-space for vertex v. If the graph has two vertices, with 15 and 20 states respectively, then entries 1 to 15 correspond to vertex 1, and entries 16 to 36 correspond to vertex 2. This compact enumeration scheme is the same as the enumeration scheme used by rotindex, rotcoord, etc

Parameters

one_body_energies - [in] - the array of one body energies

Global Read:

Global Write:

Remarks

References:

Author: apl

bool core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned ( ) const

overridevirtual

Returns true if any node in the graph is in state 0, the unassigned state.

Useful for debugging. If simulated annealing completes, and any vertex remains in state 0, then the state assignment is not meaningful nor is the energy for that assignment. The cases in which state-0 problems turn up are from passing an annealer a list of states to restrict itself to wherein some vertex has no states listed. Such cases are bugs; this subroutine helps identify them.

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::AnnealableGraphBase.

References get_node(), get_num_nodes(), and core::pack::interaction_graph::NodeBase::state_unassigned().

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

void core::pack::interaction_graph::InteractionGraphBase::blanket_assign_state_0 ( )

overridepure virtual

State initialization.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

void core::pack::interaction_graph::InteractionGraphBase::clean_up_edges_marked_for_deletion ( )

protected

Remove those edges that have marked themselves for deletion.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.irio.nosp@m.ninst.nosp@m.itut.nosp@m.e.org).

References ig_edge_list_.

Referenced by declare_all_edge_energies_final(), and prepare_graph_for_simulated_annealing().

core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::commit_considered_substitution ( )

overridepure virtual

Accept a considered substitution (i.e. make the substitution permanent; commit it).

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

void core::pack::interaction_graph::InteractionGraphBase::consider_substitution	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_energy_for_node
	)

overridepure virtual

Consider switching node "node_ind" to state "new_state".

Must be implemented by derived classes.

Parameters

[in]	node_ind	The node index.
[in]	new_state	The state index that we are considering switching TO.
[out]	delta_energy	The change in energy that results from the switch under consideration, computed by this function.
[out]	prev_energy_for_node	The energy of this node prior to the substitutio, returned by this function.

Implements core::pack::interaction_graph::AnnealableGraphBase.

int core::pack::interaction_graph::InteractionGraphBase::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.

count_connected_components_and_initialize_vertex_groups

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References component_membership_, energy_sum_group_membership_, ig_nodes_, num_energy_sum_groups_, num_ig_nodes_, and vertex_already_reached().

unsigned int core::pack::interaction_graph::InteractionGraphBase::count_dynamic_memory ( ) const

protectedvirtual

References ig_edge_list_, and num_ig_nodes_.

Referenced by core::pack::interaction_graph::DoubleDensePDInteractionGraph::count_dynamic_memory(), core::pack::interaction_graph::DensePDInteractionGraph::count_dynamic_memory(), core::pack::interaction_graph::FASTERInteractionGraph::count_dynamic_memory(), core::pack::interaction_graph::PDInteractionGraph::count_dynamic_memory(), core::pack::interaction_graph::OnTheFlyInteractionGraph::count_dynamic_memory(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::count_dynamic_memory(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::count_dynamic_memory(), and getTotalMemoryUsage().

virtual unsigned int core::pack::interaction_graph::InteractionGraphBase::count_static_memory ( ) const

protectedpure virtual

Referenced by getTotalMemoryUsage().

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

pure virtual

Referenced by add_edge().

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

pure virtual

void core::pack::interaction_graph::InteractionGraphBase::declare_all_edge_energies_final ( )

virtual

Iterates over all edges and calls declare_energies_final() on all of them. Takes O(N) time, where N is the number of edges.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References clean_up_edges_marked_for_deletion(), and ig_edge_list_.

void core::pack::interaction_graph::InteractionGraphBase::drop_all_edges_for_node ( int node )

deletes all edges adjacent to the node specified

Parameters

node	- [in] - index of the node

Global Read:

Global Write:

Remarks

References:

Author: apl

References core::pack::interaction_graph::NodeBase::drop_all_edges(), and get_node().

void core::pack::interaction_graph::InteractionGraphBase::drop_edge ( std::list< EdgeBase * >::iterator iter )

protected

removes edge from edge list at iterator iter

each edge keeps track of its position in its owner's graph's edge list so it can efficiently delete itself should it need to.

Parameters

iter	- [in] - the iterator pointing at the edge that's deleting itself

Global Read:

Global Write:

Remarks

References:

Author: apl

References focused_edge_, and ig_edge_list_.

Referenced by core::pack::interaction_graph::EdgeBase::~EdgeBase().

bool core::pack::interaction_graph::InteractionGraphBase::edge_list_iterator_at_end ( ) const

test: have we arrived at the edge list end?

References focused_edge_iterator_, and focused_edge_iterator_end_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::setup_IG_res_res_weights().

EdgeBase const * core::pack::interaction_graph::InteractionGraphBase::find_edge	(	int	node1,
		int	node2,
		bool const	use_threadsafe_lookup = `false`
	)		const

Find an edge and return a const pointer to it.

returns the edge connecting node1 and node2

The following functions provide access to the nodes and edges in the graph though, their use is strongly discouraged except for in writing unit tests to ensure that the graphs are properly implemented.

By default, the last edge accessed is cached, for faster lookups. If use_threadsafe_lookup is true, we avoid the caching.

graph keeps a pointer to the last edge that was accessed to that search is fairly efficient.

Parameters

node1	- [in] - index of the first node
node2	- [in] - index of the second node
use_threadsafe_lookup	- [in] - If true, do not cache the last edge for faster future lookup. False by default.

Global Read:

Global Write:

Remarks

References:

Author: apl

References focused_edge_, ig_nodes_, and core::pack::interaction_graph::EdgeBase::same_edge().

EdgeBase * core::pack::interaction_graph::InteractionGraphBase::find_edge	(	int	node1,
		int	node2,
		bool const	use_threadsafe_lookup = `false`
	)

Find an edge and return a nonconst pointer to it.

By default, the last edge accessed is cached, for faster lookups. If use_threadsafe_lookup is true, we avoid the caching.

References focused_edge_, ig_nodes_, and core::pack::interaction_graph::EdgeBase::same_edge().

EdgeBase const & core::pack::interaction_graph::InteractionGraphBase::get_edge ( ) const

return a const reference to an edge pointed at by the list iterator

References focused_edge_iterator_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::setup_IG_res_res_weights().

bool core::pack::interaction_graph::InteractionGraphBase::get_edge_exists	(	int	node1,
		int	node2
	)		const

returns true if an edge between node1 and node2 exists

Parameters

node1 - [in] - index of the one of the nodes node2 - [in] - index of the other node

Global Read:

Global Write:

Remarks

References:

Author: apl

References find_edge().

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

std::list< EdgeBase* >::iterator core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin ( )

inline

References ig_edge_list_.

std::list< EdgeBase* >::const_iterator core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin ( ) const

inline

References ig_edge_list_.

std::list< EdgeBase* >::iterator core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end ( )

inline

References ig_edge_list_.

std::list< EdgeBase* >::const_iterator core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end ( ) const

inline

References ig_edge_list_.

virtual int core::pack::interaction_graph::InteractionGraphBase::get_edge_memory_usage ( ) const

pure virtual

Real core::pack::interaction_graph::InteractionGraphBase::get_edge_weight	(	int	node1,
		int	node2
	)		const

returns 0 if edge is not part of the graph

References core::pack::interaction_graph::EdgeBase::edge_weight(), and find_edge().

core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::get_energy_current_state_assignment ( )

overridepure virtual

Get the energy resulting from the current set of state assignments.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

virtual core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::get_energy_sum_for_vertex_group ( int group_id )

pure virtual

NodeBase* core::pack::interaction_graph::InteractionGraphBase::get_node ( int index ) const

inline

References ig_nodes_, and num_ig_nodes_.

int core::pack::interaction_graph::InteractionGraphBase::get_node_state_offset ( int index ) const

inlineprotected

References node_state_offsets_, and num_ig_nodes_.

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states().

int core::pack::interaction_graph::InteractionGraphBase::get_num_edges ( ) const

inline

References ig_edge_list_.

Referenced by core::pack::interaction_graph::DoubleLazyInteractionGraph::prepare_graph_for_simulated_annealing(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_pose(), and protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_scorefxn().

int core::pack::interaction_graph::InteractionGraphBase::get_num_nodes ( ) const

inlineoverridevirtual

Get the number of nodes in the graph.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References num_ig_nodes_.

int core::pack::interaction_graph::InteractionGraphBase::get_num_states_for_node ( int node_index ) const

overridevirtual

returns the number of states for a particular node

Parameters

node_index - [in] - the index of the node in question

Global Read:

Global Write:

Remarks

References:

Author: apl

Implements core::pack::interaction_graph::AnnealableGraphBase.

References ig_nodes_.

int core::pack::interaction_graph::InteractionGraphBase::get_num_total_states ( ) const

inlineoverridevirtual

Get the total number of states.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References num_total_states_.

virtual core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::get_one_body_energy_for_node_state	(	int	node,
		int	state
	)

pure virtual

Implemented in core::pack::interaction_graph::SymmOnTheFlyInteractionGraph, core::pack::interaction_graph::OnTheFlyInteractionGraph, core::pack::interaction_graph::PDInteractionGraph, core::pack::interaction_graph::FASTERInteractionGraph, core::pack::interaction_graph::DensePDInteractionGraph, protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph, and core::pack::interaction_graph::DoubleDensePDInteractionGraph.

bool core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group	(	int	node_index,
		int	group_id
	)

inline

References energy_sum_group_membership_, num_energy_sum_groups_, and num_ig_nodes_.

unsigned int core::pack::interaction_graph::InteractionGraphBase::getTotalMemoryUsage ( ) const

virtual

References count_dynamic_memory(), count_static_memory(), ig_edge_list_, ig_nodes_, and num_ig_nodes_.

void core::pack::interaction_graph::InteractionGraphBase::increment_edge_list_iterator ( ) const

increment the (single) edge list iterator to the next element

References focused_edge_iterator_, and focused_edge_iterator_end_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::setup_IG_res_res_weights().

virtual void core::pack::interaction_graph::InteractionGraphBase::initialize ( pack_basic::RotamerSetsBase const & rot_sets )

pure virtual

bool core::pack::interaction_graph::InteractionGraphBase::mine ( EdgeBase const * edge ) const

inlineprotected

References core::pack::interaction_graph::EdgeBase::get_owner().

Referenced by protocols::flexpack::interaction_graph::FlexbbInteractionGraph::cast_flexbb_edge(), protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::cast_minimalist_flexbb_edge(), and protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::cast_otfflexbb_edge().

void core::pack::interaction_graph::InteractionGraphBase::note_vertex_reached ( int node_index )

marks a vertex as belonging to the connected component currently being traversed in the depth first traversal.

Parameters

node_index - [in] - the index of the node invoking this method.

Global Read:

Global Write:

Remarks: This method should be used by the NodeBase class only.

References:

Author: apl

References component_membership_, and num_energy_sum_groups_.

Referenced by core::pack::interaction_graph::NodeBase::depth_first_connected_component_counting().

InteractionGraphBase& core::pack::interaction_graph::InteractionGraphBase::operator= ( InteractionGraphBase const & )

private

void core::pack::interaction_graph::InteractionGraphBase::output_connectivity ( std::ostream & os ) const

writes out a list of all the edges in the graph

Parameters

os	- [in] - the output stream to write to

Global Read:

Global Write:

Remarks

References:

Author: apl

References ig_edge_list_.

void core::pack::interaction_graph::InteractionGraphBase::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)

Parameters

os	- [in] - the output stream to write to

Global Read:

Global Write:

Remarks

References:

Author: apl

References ig_edge_list_, and num_ig_nodes_.

void core::pack::interaction_graph::InteractionGraphBase::prepare_graph_for_simulated_annealing ( )

overridevirtual

iterate across edges and nodes and allow them to prepare for simulated annealing

Edges may decide to delete themselves during this subroutine; therefore edges are prepared first. Afterwards, the nodes must update their edge vector representation.

Implements core::pack::interaction_graph::AnnealableGraphBase.

Reimplemented in core::pack::interaction_graph::LinearMemoryInteractionGraph, core::pack::interaction_graph::SymmLinearMemoryInteractionGraph, and core::pack::interaction_graph::SymmMinimalistInteractionGraph.

References clean_up_edges_marked_for_deletion(), get_edge_list_begin(), get_edge_list_end(), get_node(), get_num_nodes(), and core::pack::interaction_graph::NodeBase::prepare_for_simulated_annealing().

Referenced by core::pack::interaction_graph::SymmMinimalistInteractionGraph::prepare_graph_for_simulated_annealing(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::prepare_graph_for_simulated_annealing(), core::pack::interaction_graph::LinearMemoryInteractionGraph::prepare_graph_for_simulated_annealing(), and core::pack::interaction_graph::DoubleLazyInteractionGraph::prepare_graph_for_simulated_annealing().

virtual void core::pack::interaction_graph::InteractionGraphBase::print ( ) const

inlinevirtual

virtual void core::pack::interaction_graph::InteractionGraphBase::print_current_state_assignment ( ) const

pure virtual

void core::pack::interaction_graph::InteractionGraphBase::print_vertex_groups ( )

References energy_sum_group_membership_, get_num_nodes(), and num_energy_sum_groups_.

void core::pack::interaction_graph::InteractionGraphBase::print_vertices ( ) const

calls print() on each of the nodes in the graph

Parameters

par Global Read:

Global Write:

Remarks

References:

Author: apl

References ig_nodes_, and num_ig_nodes_.

void core::pack::interaction_graph::InteractionGraphBase::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

Methods for iterating across edges of the interaction graph. Protected access since the raw edge lists contain non-const pointers.

References focused_edge_iterator_, focused_edge_iterator_end_, and ig_nodes_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::setup_IG_res_res_weights().

void core::pack::interaction_graph::InteractionGraphBase::set_edge_weight	(	int	node1,
		int	node2,
		Real	edge_weight
	)

invokes polymorphic method of EdgeBase class; no-op if edge is not part of the graph.

References find_edge(), and core::pack::interaction_graph::EdgeBase::set_edge_weight().

Referenced by core::pack::interaction_graph::InteractionGraphFactory::setup_IG_res_res_weights().

void core::pack::interaction_graph::InteractionGraphBase::set_errorfull_deltaE_threshold ( core::PackerEnergy deltaE )

overridepure virtual

Set an error threshold.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::set_network_state ( ObjexxFCL::FArray1_int & node_states )

overridepure virtual

Explicit state modification for the network.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

void core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node	(	int	node_index,
		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.

once the graph knows how many states a node has, it instantiates a new node using the NodeBase(int) constructor through the graph's factory method create_new_node()

Parameters

node_index	- [in] - the index of the node
num_states	- [in] - the number of states for that node

Global Read:

Global Write:

Remarks

References:

Author: apl

Referenced by core::pack::interaction_graph::DoubleDensePDInteractionGraph::initialize(), core::pack::interaction_graph::DensePDInteractionGraph::initialize(), core::pack::interaction_graph::OnTheFlyInteractionGraph::initialize(), core::pack::interaction_graph::FASTERInteractionGraph::initialize(), core::pack::interaction_graph::PDInteractionGraph::initialize(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::initialize(), and protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize().

void core::pack::interaction_graph::InteractionGraphBase::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.)

First you must declare how many groups you are interested in. Do that with this method. Second you must declare which node is a member of each group. Only tell the graph which node is a member, do not tell the graph if a node is not a member. Third, when you want to know the energy sum for the group in the graph's current state assignment, call get_energy_sum_for_vertex_group( group_id)

Parameters

num_groups - [in] - the number of groups; set this at most once.

Global Read:

Global Write:

Remarks

References:

Author: apl

References energy_sum_group_membership_, num_energy_sum_groups_, and num_ig_nodes_.

void core::pack::interaction_graph::InteractionGraphBase::set_onebody_energies_multithreaded	(	core::Size const	node_index,
		core::pack::rotamer_set::RotamerSetCOP	rotset,
		core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		task::PackerTask const &	task,
		utility::graph::GraphCOP	packer_neighbor_graph,
		basic::thread_manager::RosettaThreadAssignmentInfo const &	thread_assignments
	)

Compute and store the onebody energy for all rotamers at a position. Safe for a multithreaded context.

Requires that the number of states was already set.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References add_to_nodes_one_body_energy(), num_ig_nodes_, and core::pack::interaction_graph::TR().

core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::set_state_for_node	(	int	node_ind,
		int	new_state
	)

overridepure virtual

Explicit state modification for a node.

Must be implemented by derived classes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

void core::pack::interaction_graph::InteractionGraphBase::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.)

tell the graph which vertices you want to be part of which groups

Parameters

vertex - [in] - the index of the vertex you wish to include in the group group - [in] - the group index you wish to add the vertex to.

Global Read:

Global Write:

Remarks

References:

Author: apl

References energy_sum_group_membership_.

void core::pack::interaction_graph::InteractionGraphBase::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.

Parameters

old_energy1b - [in/out] - the one body energies representing interactions with portions of the background that are no longer valid new_energy1b - [in] - the one body energies representing interactions with the background after the background has changed

Global Read:

Global Write:

Remarks: useful if you want to move something in the background like a ligand. moving the background does not invalidate the two-body energies.

References:

Author: apl

bool core::pack::interaction_graph::InteractionGraphBase::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.

vertex_already_reached

Parameters

node_index - [in] - the index of the node calling the method.