#include <PDInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::PDInteractionGraph:

Public Member Functions
	PDInteractionGraph (int num_nodes)
	main constructor: no default nor copy constructors provided. More...

void	initialize (pack_basic::RotamerSetsBase const &rot_sets) override

core::PackerEnergy	get_one_body_energy_for_node_state (int node, int state) override
	accessor More...

int	get_num_aatypes () const override
	sets the number of amino acid types present. More...

virtual void	add_edge (int node1, int node2)

void	blanket_assign_state_0 () override
	assigns the state of all nodes in the interaction graph to their unassigned or zero states. More...

core::PackerEnergy	set_state_for_node (int node_ind, int new_state) override
	sets the state on node node_ind to new_state More...

core::PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states) override
	takes in a vector of states, one state per node, and sets the state for each of the nodes to the specified state. More...

void	consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override
	considers altering the state of a particular node; returns the change in energy that the state substitution would produce More...

core::PackerEnergy	commit_considered_substitution () override
	Accepts (commits) the state change previously considered in a call to consider_substitution and returns the energy of the entire graph. More...

core::PackerEnergy	get_energy_current_state_assignment () override
	@ brief O(1) total energy report. Protected read access for derived classes. More...

int	get_edge_memory_usage () const override
	older scheme for memory accounting – replace this asap More...

void	print_current_state_assignment () const override
	outputs the current state for each node, useful for debugging More...

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

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override

core::PackerEnergy	get_energy_sum_for_vertex_group (int group_id) override
	a user may define subsets of the vertex set for which they would like to know the internal energy sum. More...

core::PackerEnergy	get_weighted_energy (ObjexxFCL::FArray2D< core::PackerEnergy > const &weights) const

core::PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states, ObjexxFCL::FArray2D< core::PackerEnergy > const &weights)

virtual void	consider_substitution (int node_ind, int new_state, core::PackerEnergy &deltaE_unweighted, core::PackerEnergy &prevE_unweighted, core::PackerEnergy &deltaE_weighted, core::PackerEnergy &prevE_weighted, ObjexxFCL::FArray2D< core::PackerEnergy > const &weights)

virtual core::PackerEnergy	commit_considered_substitution (ObjexxFCL::FArray2D< core::PackerEnergy > const &weights)

bool	aa_submatrix_energies_retrievable () const override
	Override the InteractionGraphBase class's implementation of this function to return 'true'. More...

int	aatype_for_node_state (int node_ind, int node_state) const override

ObjexxFCL::FArray2D < core::PackerEnergy >	get_aa_submatrix_energies_for_edge (int node1, int node2, int node1aa, int node2aa) const override

Public Member Functions inherited from core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
	~PrecomputedPairEnergiesInteractionGraph () override

	PrecomputedPairEnergiesInteractionGraph (int num_nodes)

void	add_to_two_body_energies_for_edge (int node1, int node2, ObjexxFCL::FArray2< core::PackerEnergy > const &res_res_energy_array, bool const use_threadsafe_method=false)
	interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies More...

void	add_to_two_body_energies_for_edge (int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy)
	interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies More...

void	set_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy)
	interface to PDEdge::set_two_body_energy More...

void	clear_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2)
	interface to PDEdge::clear_two_body_energy More...

void	set_twobody_energies_multithreaded (std::pair< core::Size, core::Size > const &nodes, std::pair< core::pack::rotamer_set::RotamerSetCOP, core::pack::rotamer_set::RotamerSetCOP > rotsets, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_info, bool const finalize_edges, core::conformation::symmetry::SymmetryInfoCOP symminfo, std::pair< core::Size, core::Size > const &resids, bool const do_orient, bool const symmetric_swap)
	Given two nodes, compute the energy of all interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context. More...

void	add_longrange_twobody_energies_multithreaded (std::pair< core::Size, core::Size > const &nodes, std::pair< core::pack::rotamer_set::RotamerSetCOP, core::pack::rotamer_set::RotamerSetCOP > rotsets, core::pose::Pose const &pose, core::scoring::methods::LongRangeTwoBodyEnergyCOP lr_energy, core::scoring::ScoreFunction const &sfxn, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_info, bool const finalize_edges, core::conformation::symmetry::SymmetryInfoCOP symminfo, std::pair< core::Size, core::Size > const &resids, bool const do_orient, bool const symmetric_swap)
	Given two nodes and a long-range energy, compute the long-range energy of all interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context. More...

virtual void	declare_edge_energies_final (int node1, int node2, bool const use_threadsafe_lookup=false)
	call this if you're done storing energies in an edge - it will reduce the memory usage for that edge if possible More...

Public Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph
	~FixedBBInteractionGraph () override

	FixedBBInteractionGraph (int num_nodes)

void	set_sparse_aa_info_for_edge (int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info)
	interface to PDEdge::set_sparse_aa_info More...

bool	get_sparse_aa_info_for_edge (int node1, int node2, int node1aa, int node2aa)
	returns true if node1aa and node2aa are amino acid neighbors More...

void	force_aa_neighbors_for_edge (int node1, int node2, int node1aa, int node2aa)
	interface to FixedBBEdge::force_aa_neighbors More...

void	force_all_aa_neighbors_for_edge (int node1, int node2)
	interface to PDEdge::force_aa_neighbors More...

virtual core::PackerEnergy	get_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2) const
	interface to FixedBBEdge::get_two_body_energy More...

Public Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase
	~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...

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...

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	set_edge_weight (int node1, int node2, Real edge_weight)

Real	get_edge_weight (int node1, int node2) const

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 ()

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...

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
virtual unsigned int	getMemoryUsageInBytes () const

NodeBase *	create_new_node (int node_index, int num_states) override
	factory method that instantiates a PDNode. More...

EdgeBase *	create_new_edge (int index1, int index2) override
	factory method that instantiates a PDEdge More...

core::PackerEnergy	get_energy_PD_current_state_assignment ()

void	update_internal_energy_totals ()
	removes numerical drift that can accumulate over the course of many state assignment changes within simulated annealing More...

PDNode *	get_pd_node (int index) const

PDEdge const *	get_pd_edge (int node1, int node2) const

PDEdge *	get_pd_edge (int node1, int node2)

Protected Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph
FixedBBNode const *	get_fixedbb_node (int node_index) const
	Downcasts. More...

FixedBBNode *	get_fixedbb_node (int node_index)

FixedBBEdge const *	get_fixedbb_edge (int node1, int node2) const

FixedBBEdge *	get_fixedbb_edge (int node1, int node2)

Protected Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase
void	clean_up_edges_marked_for_deletion ()
	Remove those edges that have marked themselves for deletion. More...

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
	PDInteractionGraph ()

	PDInteractionGraph (PDInteractionGraph const &)

PDInteractionGraph &	operator= (PDInteractionGraph const &)

Private Attributes
int	num_aa_types_

int	num_commits_since_last_update_

core::PackerEnergy	total_energy_current_state_assignment_

core::PackerEnergy	total_energy_alternate_state_assignment_

int	node_considering_alt_state_

int	num_nodes_in_file_

int	num_file_aa_types_

ObjexxFCL::FArray1D_int	file_node_2_instance_node_

ObjexxFCL::FArray1D_int	instance_node_2_file_node_

ObjexxFCL::FArray1D < ObjexxFCL::FArray1D_int >	aa_types_for_states_on_file_nodes_

ObjexxFCL::FArray1D < ObjexxFCL::FArray1D_int >	num_file_states_for_aa_for_node_

Static Private Attributes
static const int	COMMIT_LIMIT_BETWEEN_UPDATES = 1024

Constructor & Destructor Documentation

core::pack::interaction_graph::PDInteractionGraph::PDInteractionGraph ( int num_nodes )

main constructor: no default nor copy constructors provided.

Parameters

num_nodes - [in] - the number of nodes in this graph

core::pack::interaction_graph::PDInteractionGraph::PDInteractionGraph ( )

private

Referenced by count_static_memory(), and getMemoryUsageInBytes().

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

private

Member Function Documentation

bool core::pack::interaction_graph::PDInteractionGraph::aa_submatrix_energies_retrievable ( ) const

overridevirtual

Override the InteractionGraphBase class's implementation of this function to return 'true'.

PDInteractionGraph will return aa submatrices as requested.

Reimplemented from core::pack::interaction_graph::FixedBBInteractionGraph.

int core::pack::interaction_graph::PDInteractionGraph::aatype_for_node_state	(	int	node_ind,
		int	node_state
	)		const

overridevirtual

Derived classes wishing to respond to the get_aa_submatrix_energies_for_edge must implement this function as well, which allows the mapping between states and their on-node amino-acid index (which may very well represent something other than the index of the enumeration element for the rotamer's "aa()").

Reimplemented from core::pack::interaction_graph::FixedBBInteractionGraph.

References core::pack::interaction_graph::PDNode::aatype_for_state(), and get_pd_node().

void core::pack::interaction_graph::PDInteractionGraph::add_edge	(	int	node1,
		int	node2
	)

virtual

References core::pack::interaction_graph::InteractionGraphBase::add_edge(), core::pack::interaction_graph::PDEdge::force_all_aa_neighbors(), and get_pd_edge().

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

overridevirtual

assigns the state of all nodes in the interaction graph to their unassigned or zero states.

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

References core::pack::interaction_graph::PDNode::assign_zero_state(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_pd_node(), and total_energy_current_state_assignment_.

float core::pack::interaction_graph::PDInteractionGraph::commit_considered_substitution ( )

overridevirtual

Accepts (commits) the state change previously considered in a call to consider_substitution and returns the energy of the entire graph.

to avoid too much numerical drift from accumulating, the bookkeeping arrays are updated once every 2^10 state commits

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

References COMMIT_LIMIT_BETWEEN_UPDATES, get_pd_node(), node_considering_alt_state_, num_commits_since_last_update_, total_energy_alternate_state_assignment_, total_energy_current_state_assignment_, and update_internal_energy_totals().

Referenced by commit_considered_substitution().

float core::pack::interaction_graph::PDInteractionGraph::commit_considered_substitution ( ObjexxFCL::FArray2D< core::PackerEnergy > const & weights )

virtual

References commit_considered_substitution(), and get_weighted_energy().

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

overridevirtual

considers altering the state of a particular node; returns the change in energy that the state substitution would produce

To avoid too much numerical drift from accumulating, the bookkeeping arrays are updated once every 2^10 state commits

Parameters

node_ind	- [in] - the index of the node considering a state change
new_state	- [in] - the new state that node is considering
alt_total_energy	- [out] - the total network energy produced under the new state
delta_energy	- [out] - the change in energy produced under the substitution
prev_energy_for_node	- [out] - the sum of the one and two body energies for this node under the current state assignment

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

void core::pack::interaction_graph::PDInteractionGraph::consider_substitution	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	deltaE_unweighted,
		core::PackerEnergy &	prevE_unweighted,
		core::PackerEnergy &	deltaE_weighted,
		core::PackerEnergy &	prevE_weighted,
		ObjexxFCL::FArray2D< core::PackerEnergy > const &	weights
	)

virtual

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

overridevirtual

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

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

unsigned int core::pack::interaction_graph::PDInteractionGraph::count_static_memory ( ) const

overridevirtual

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

References PDInteractionGraph().

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

overrideprotectedvirtual

factory method that instantiates a PDEdge

Parameters

index1	- [in] - the smaller-indexed node this edge is incident upon
index2	- [in] - the larger-indexed node this edge is incident upon

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

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

overrideprotectedvirtual

factory method that instantiates a PDNode.

Parameters

node_index	- [in] - the index of the node being created
num_states	- [in] - the total number of states for the new node

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

ObjexxFCL::FArray2D< core::PackerEnergy > core::pack::interaction_graph::PDInteractionGraph::get_aa_submatrix_energies_for_edge	(	int	node1,
		int	node2,
		int	node1aa,
		int	node2aa
	)		const

overridevirtual

Do not call this function unless it is implemented in the derived class, as should be indicated by the "aa_submatrix_energies_retrivable" method.

Reimplemented from core::pack::interaction_graph::FixedBBInteractionGraph.

References core::pack::interaction_graph::PDEdge::get_aa_submatrix_energies(), and get_pd_edge().

int core::pack::interaction_graph::PDInteractionGraph::get_edge_memory_usage ( ) const

overridevirtual

older scheme for memory accounting – replace this asap

returns the number of floats used in all edge two-body energy tables

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

References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), and core::simple_metrics::metrics::sum.

float core::pack::interaction_graph::PDInteractionGraph::get_energy_current_state_assignment ( )

overridevirtual

@ brief O(1) total energy report. Protected read access for derived classes.

removes all accumulated numerical drift and returns the energy for the current state assignment.

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

References total_energy_current_state_assignment_, and update_internal_energy_totals().

float core::pack::interaction_graph::PDInteractionGraph::get_energy_PD_current_state_assignment ( )

protected

References total_energy_current_state_assignment_.

float core::pack::interaction_graph::PDInteractionGraph::get_energy_sum_for_vertex_group ( int group_id )

overridevirtual

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.). ask the graph for the energies of the induced subgraph defined by a particular group.

Parameters

group_id - [in] - the groups for which you're interested in retrieving energies of the induced subgraph

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

References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), core::pack::interaction_graph::PDNode::get_one_body_energy_current_state(), get_pd_node(), and core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group().

int core::pack::interaction_graph::PDInteractionGraph::get_num_aatypes ( ) const

overridevirtual

sets the number of amino acid types present.

returns the number of different amino acid types

The actual meaning of the integers used to represent amino acid types is not important, rather each state is labeled as being of some amino acid type. The amino acid types mean little more than equivalence classes; two states are either in the same equivalence class or they are in different ones. this function should be called once and only once

Parameters

num_aa_types - [in] - the number of amino acid types

Implements core::pack::interaction_graph::FixedBBInteractionGraph.

References num_aa_types_.

float core::pack::interaction_graph::PDInteractionGraph::get_one_body_energy_for_node_state	(	int	node,
		int	state
	)

overridevirtual

accessor

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

References core::pack::interaction_graph::PDNode::get_one_body_energy(), and get_pd_node().

Referenced by core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds().

PDEdge const* core::pack::interaction_graph::PDInteractionGraph::get_pd_edge	(	int	node1,
		int	node2
	)		const

inlineprotected

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

Referenced by add_edge(), and get_aa_submatrix_energies_for_edge().

PDEdge* core::pack::interaction_graph::PDInteractionGraph::get_pd_edge	(	int	node1,
		int	node2
	)

inlineprotected

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

PDNode* core::pack::interaction_graph::PDInteractionGraph::get_pd_node ( int index ) const

inlineprotected

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

Referenced by aatype_for_node_state(), blanket_assign_state_0(), commit_considered_substitution(), get_energy_sum_for_vertex_group(), get_one_body_energy_for_node_state(), get_weighted_energy(), initialize(), print_current_state_assignment(), set_network_state(), set_state_for_node(), and update_internal_energy_totals().

float core::pack::interaction_graph::PDInteractionGraph::get_weighted_energy ( ObjexxFCL::FArray2D< core::PackerEnergy > const & weights ) const

References core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_pd_node(), and core::pack::interaction_graph::PDNode::get_weighted_energy_with_higher_indexed_nodes().

Referenced by commit_considered_substitution(), and set_network_state().

unsigned int core::pack::interaction_graph::PDInteractionGraph::getMemoryUsageInBytes ( ) const

protectedvirtual

References PDInteractionGraph().

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

overridevirtual

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

References get_pd_node(), num_aa_types_, core::pack::interaction_graph::PDNode::set_amino_acid_types(), and core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node().

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

private

void core::pack::interaction_graph::PDInteractionGraph::print_current_state_assignment ( ) const

overridevirtual

outputs the current state for each node, useful for debugging

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

References core::pack::interaction_graph::PDNode::get_current_state(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_pd_node(), and core::pack::interaction_graph::PDNode::print_internal_energies().

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

inlineoverridevirtual

Set an error threshold.

Must be implemented by derived classes.

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

float core::pack::interaction_graph::PDInteractionGraph::set_network_state ( ObjexxFCL::FArray1_int & node_states )

overridevirtual

takes in a vector of states, one state per node, and sets the state for each of the nodes to the specified state.

also calls "update internal energy totals" to undo any numerical noise accumulated during the transition.

Parameters

node_states - [in] - array of states, one for each node.

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

References core::pack::interaction_graph::PDNode::assign_state(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_pd_node(), total_energy_current_state_assignment_, and update_internal_energy_totals().

Referenced by set_network_state().

float core::pack::interaction_graph::PDInteractionGraph::set_network_state	(	ObjexxFCL::FArray1_int &	node_states,
		ObjexxFCL::FArray2D< core::PackerEnergy > const &	weights
	)

References get_weighted_energy(), and set_network_state().

float core::pack::interaction_graph::PDInteractionGraph::set_state_for_node	(	int	node_ind,
		int	new_state
	)

overridevirtual

sets the state on node node_ind to new_state

Parameters

node_ind	- [in] - the index of the node in question
new_state	- [in] - the new state the node is being assigned to

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

References core::pack::interaction_graph::PDNode::assign_state(), get_pd_node(), total_energy_current_state_assignment_, and update_internal_energy_totals().

void core::pack::interaction_graph::PDInteractionGraph::update_internal_energy_totals ( )

protected

removes numerical drift that can accumulate over the course of many state assignment changes within simulated annealing

Iterates across nodes and then edges to look-up the energies for the current state assignmnet removing any numerical drift which accumulated in the member variable total_energy_current_state_assignment_.

References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_pd_node(), num_commits_since_last_update_, and total_energy_current_state_assignment_.

Referenced by commit_considered_substitution(), get_energy_current_state_assignment(), set_network_state(), and set_state_for_node().

Member Data Documentation

ObjexxFCL::FArray1D< ObjexxFCL::FArray1D_int > core::pack::interaction_graph::PDInteractionGraph::aa_types_for_states_on_file_nodes_

private

const int core::pack::interaction_graph::PDInteractionGraph::COMMIT_LIMIT_BETWEEN_UPDATES = 1024

staticprivate

Referenced by commit_considered_substitution().

ObjexxFCL::FArray1D_int core::pack::interaction_graph::PDInteractionGraph::file_node_2_instance_node_

private

ObjexxFCL::FArray1D_int core::pack::interaction_graph::PDInteractionGraph::instance_node_2_file_node_

private

int core::pack::interaction_graph::PDInteractionGraph::node_considering_alt_state_

private

Referenced by commit_considered_substitution().

int core::pack::interaction_graph::PDInteractionGraph::num_aa_types_

private

Referenced by get_num_aatypes(), and initialize().

int core::pack::interaction_graph::PDInteractionGraph::num_commits_since_last_update_

private

Referenced by commit_considered_substitution(), and update_internal_energy_totals().

int core::pack::interaction_graph::PDInteractionGraph::num_file_aa_types_

private

ObjexxFCL::FArray1D< ObjexxFCL::FArray1D_int > core::pack::interaction_graph::PDInteractionGraph::num_file_states_for_aa_for_node_

private

int core::pack::interaction_graph::PDInteractionGraph::num_nodes_in_file_

private

core::PackerEnergy core::pack::interaction_graph::PDInteractionGraph::total_energy_alternate_state_assignment_

private

Referenced by commit_considered_substitution().

core::PackerEnergy core::pack::interaction_graph::PDInteractionGraph::total_energy_current_state_assignment_

private

Referenced by blanket_assign_state_0(), commit_considered_substitution(), get_energy_current_state_assignment(), get_energy_PD_current_state_assignment(), set_network_state(), set_state_for_node(), and update_internal_energy_totals().

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

src/core/pack/interaction_graph/PDInteractionGraph.hh
src/core/pack/interaction_graph/PDInteractionGraph.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation