#include <HBondGraphInitializerIG.hh>

Inheritance diagram for core::pack::hbonds::HBondGraphInitializerIG:

[legend]

Public Member Functions
	HBondGraphInitializerIG (scoring::hbonds::graph::HBondGraphOP hbond_graph, rotamer_set::RotamerSetsCOP rotamer_sets, float hbond_threshold, float clash_threshold)

	~HBondGraphInitializerIG () override

void	eval_rot_pair (unsigned int const global_rot1, unsigned int const global_rot2, PackerEnergy const two_body_energy)
	look for hbonds and clashes More...

interaction_graph::EdgeBase *	create_new_edge (int index1, int index2) override

rotamer_set::RotamerSetsCOP	rotamer_sets ()

void	finalize_hbond_graph ()

PackerEnergy	get_two_body_energy_for_edge (int, int, int, int) const override
	Exits if this is called. More...

void	find_symmetric_hbonds (conformation::symmetry::SymmetryInfo const &symm_info, pose::Pose const &pose, Real hb_threshold)
	only twobody energies will get turned into edges. If you are running with symmetry, you need to call this to find edges between resids and their symmetric twins. Must be called after scoring. More...

Public Member Functions inherited from core::pack::interaction_graph::PDInteractionGraph
	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...

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...

Private Member Functions
Size	get_ind_res (pose::Pose const &pose, Size const res_i, conformation::symmetry::SymmetryInfo const &symm_info, std::map< char, std::pair< Size, Size > > &chain_bounds) const
	utility function stolen from HBNet.cc. Calculates independent resid for symmetric resid. More...

Private Attributes
std::unordered_map< std::pair< uint32_t, uint32_t >, float, boost::hash< std::pair< uint32_t, uint32_t > > >	future_edges_

scoring::hbonds::graph::HBondGraphOP	hbond_graph_

rotamer_set::RotamerSetsCOP	rotamer_sets_

float	hbond_threshold_

float	clash_threshold_

Additional Inherited Members
Protected Member Functions inherited from core::pack::interaction_graph::PDInteractionGraph
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

Constructor & Destructor Documentation

◆ HBondGraphInitializerIG()

core::pack::hbonds::HBondGraphInitializerIG::HBondGraphInitializerIG	(	scoring::hbonds::graph::HBondGraphOP	hbond_graph,
		rotamer_set::RotamerSetsCOP	rotamer_sets,
		float	hbond_threshold,
		float	clash_threshold
	)

◆ ~HBondGraphInitializerIG()

core::pack::hbonds::HBondGraphInitializerIG::~HBondGraphInitializerIG ( )

overridedefault

Member Function Documentation

◆ create_new_edge()

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

inlineoverridevirtual

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

◆ eval_rot_pair()

void core::pack::hbonds::HBondGraphInitializerIG::eval_rot_pair	(	unsigned int const	global_rot1,
		unsigned int const	global_rot2,
		PackerEnergy const	two_body_energy
	)

look for hbonds and clashes

References clash_threshold_, future_edges_, hbond_graph_, hbond_threshold_, core::scoring::hbonds::graph::HBondNode::register_clash(), protocols::jumping::rot1, protocols::jumping::rot2, and core::id::swap().

◆ finalize_hbond_graph()

void core::pack::hbonds::HBondGraphInitializerIG::finalize_hbond_graph ( )

References future_edges_, hbond_graph_, protocols::jumping::rot1, protocols::jumping::rot2, core::scoring::hbonds::graph::HBondEdge::set_energy(), and protocols::hybridization::val.

◆ find_symmetric_hbonds()

void core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds	(	conformation::symmetry::SymmetryInfo const &	symm_info,
		pose::Pose const &	pose,
		Real	hb_threshold
	)

only twobody energies will get turned into edges. If you are running with symmetry, you need to call this to find edges between resids and their symmetric twins. Must be called after scoring.

References core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), get_ind_res(), core::pack::interaction_graph::PDInteractionGraph::get_one_body_energy_for_node_state(), hbond_graph_, core::conformation::symmetry::SymmetryInfo::is_asymmetric_seqpos(), rot(), rotamer_sets_, core::conformation::symmetry::SymmetryInfo::score_multiply_factor(), and core::scoring::hbonds::graph::HBondEdge::set_energy().

Referenced by protocols::hbnet::HBNet::MC_traverse_IG().

◆ get_ind_res()

Size core::pack::hbonds::HBondGraphInitializerIG::get_ind_res	(	pose::Pose const &	pose,
		Size const	res_i,
		conformation::symmetry::SymmetryInfo const &	symm_info,
		std::map< char, std::pair< Size, Size > > &	chain_bounds
	)		const

private

utility function stolen from HBNet.cc. Calculates independent resid for symmetric resid.

References core::pose::Pose::chain(), core::conformation::symmetry::SymmetryInfo::get_component_bounds(), core::conformation::symmetry::SymmetryInfo::get_component_of_residue(), core::conformation::symmetry::SymmetryInfo::get_num_components(), and core::conformation::symmetry::SymmetryInfo::num_independent_residues().

Referenced by find_symmetric_hbonds().

◆ get_two_body_energy_for_edge()

PackerEnergy core::pack::hbonds::HBondGraphInitializerIG::get_two_body_energy_for_edge	(	int	,
		int	,
		int	,
		int
	)		const

inlineoverridevirtual

Exits if this is called.

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

◆ rotamer_sets()

rotamer_set::RotamerSetsCOP core::pack::hbonds::HBondGraphInitializerIG::rotamer_sets ( )

inline

References rotamer_sets_.

Referenced by core::pack::hbonds::BareMinimumPDEdge::add_to_two_body_energies(), and core::pack::hbonds::BareMinimumPDEdge::add_to_two_body_energy().

Member Data Documentation

◆ clash_threshold_

float core::pack::hbonds::HBondGraphInitializerIG::clash_threshold_

private

Referenced by eval_rot_pair().

◆ future_edges_

std::unordered_map< std::pair< uint32_t, uint32_t >, float, boost::hash< std::pair< uint32_t, uint32_t > > > core::pack::hbonds::HBondGraphInitializerIG::future_edges_

private

Referenced by eval_rot_pair(), and finalize_hbond_graph().

◆ hbond_graph_

scoring::hbonds::graph::HBondGraphOP core::pack::hbonds::HBondGraphInitializerIG::hbond_graph_

private

Referenced by eval_rot_pair(), finalize_hbond_graph(), and find_symmetric_hbonds().

◆ hbond_threshold_

float core::pack::hbonds::HBondGraphInitializerIG::hbond_threshold_

private

Referenced by eval_rot_pair().

◆ rotamer_sets_

rotamer_set::RotamerSetsCOP core::pack::hbonds::HBondGraphInitializerIG::rotamer_sets_

private

Referenced by find_symmetric_hbonds(), and rotamer_sets().

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

src/core/pack/hbonds/HBondGraphInitializerIG.hh
src/core/pack/hbonds/HBondGraphInitializerIG.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ HBondGraphInitializerIG()

◆ ~HBondGraphInitializerIG()

Member Function Documentation

◆ create_new_edge()

◆ eval_rot_pair()

◆ finalize_hbond_graph()

◆ find_symmetric_hbonds()

◆ get_ind_res()

◆ get_two_body_energy_for_edge()

◆ rotamer_sets()

Member Data Documentation

◆ clash_threshold_

◆ future_edges_

◆ hbond_graph_

◆ hbond_threshold_

◆ rotamer_sets_