Classes
class	BareMinimumPDEdge

class	HBondGraphInitializerIG

Typedefs
using	HBondGraphInitializerIGOP = utility::pointer::shared_ptr< HBondGraphInitializerIG >

using	HBondGraphInitializerIGCOP = utility::pointer::shared_ptr< HBondGraphInitializerIG const >

Functions
scoring::hbonds::graph::HBondGraphOP	create_init_and_create_edges_for_hbond_graph (rotamer_set::RotamerSetsOP rotamer_sets, scoring::ScoreFunction const &sfxn, pose::Pose const &pose, Real hydrogen_bond_threshold, Real clash_threshold, Real hbond_energy_threshold_for_satisfaction=-0.25f, bool include_backbone_at_atom_level=false)
	Construct atom level hbond graph, initialize the node information, score rotamers to create hbonds. This will not work perfectly if you are using symmetry because it does not score one-body interactions, but can still provide a good template. More...

void	init_node_info (scoring::hbonds::graph::HBondGraph &graph, rotamer_set::RotamerSets const &rotamer_sets)
	This should be called immediately after creating the graph (and setting the number of nodes if need-be). This adds rotamer_sets info to the nodes for easier lookup later. Technically optional but recommended. More...

void	find_hbonds_in_residue_pair (conformation::Residue const &resA, conformation::Residue const &resB, scoring::hbonds::HBondDatabase const &database, utility::graph::Graph const &tenA_neighbor_graph, scoring::hbonds::HBondSet &set)
	Utility function used by other functions in this file. Given that an edge exists between two nodes, find all of the hbonds between those two residues. It does not matter which order resA and resB are. Output hbonds are put in the HBondSet provided. This should not be called before the graph is populated with edges (see HBondGraphInitializerIG) - nothing will crash if this is called with no edges but it just does not make sense. More...

void	determine_atom_level_edge_info_for_all_edges (scoring::hbonds::graph::HBondGraph &hb_graph, rotamer_set::RotamerSets const &rotamer_sets, scoring::hbonds::HBondDatabase const &database, utility::graph::Graph const &tenA_neighbor_graph, pose::Pose const &pose, bool skip_edges_with_degree_zero=false, Real hbond_energy_threshold_for_satisfaction=-0.25, conformation::symmetry::SymmetryInfoCOP symm_info=nullptr)
	Iterate through edges and calls determine_atom_level_edge_info(). skip_edges_with_degree_zero does not evaluate edges that have no incident edges and can not be part of a hydrogen bond network. symm_info needs to be != 0 if and only if you want to evaluate symmetry. More...

Size	get_symm_ind_res (pose::Pose const &pose, Size const resid, conformation::symmetry::SymmetryInfoCOP symm_info, std::map< char, std::pair< Size, Size > > chain_bounds)

void	determine_atom_level_edge_info (scoring::hbonds::graph::HBondEdge &hb_edge, rotamer_set::RotamerSets const &rotamer_sets, scoring::hbonds::HBondDatabase const &database, utility::graph::Graph const &tenA_neighbor_graph, pose::Pose const &pose, Real hbond_energy_threshold_for_satisfaction=-0.25, conformation::symmetry::SymmetryInfoCOP symm_info=nullptr)
	Add information regarding the atoms participating in hbonds (see find_hbonds_in_residue_pair() ). symm_info needs to be != 0 if and only if you want to evaluate symmetry. More...

void	determine_atom_level_node_info_for_all_nodes (scoring::hbonds::graph::HBondGraph &hb_graph, rotamer_set::RotamerSets const &rotamer_sets, utility::vector1< bool > const &include_these_resids, bool skip_nodes_with_no_edges=false, bool include_backbone=false)
	Calls determine_atom_level_node_info() for all nodes. skip_nodes_with_no_edges is recommended to be set to true but depends on your protocol. The default is false for safety purposes. More...

void	determine_atom_level_node_info (scoring::hbonds::graph::HBondNode &node, rotamer_set::RotamerSets const &rotamer_sets, utility::vector1< bool > const &include_these_resids, bool include_backbone=false)
	Store atom information for every node with a corresponding resid set to true in include_these_resids. include_these_resids was originally meant to protray "resid_is_buried" so that we only store atom info for buried residues. I don't care what you use this for so I gave it a more generalized name. More...

void	find_satisfying_interactions_with_background (scoring::hbonds::graph::HBondNode &node, rotamer_set::RotamerSets const &rotamer_sets, utility::graph::Graph const &packer_neighbor_graph, pose::Pose const &poly_ala_pose, Real hbond_energy_threshold_for_satisfaction=-0.25)
	CALL determine_atom_level_node_info() OR determine_atom_level_node_info_for_all_nodes() BEFORE CALLING THIS! After adding atom info to nodes, calling this function will result in removing atom info for atoms that hydrogen bond with the backbone or fixed sidechains. More...

void	delete_edges_with_degree_zero (scoring::hbonds::graph::HBondGraph &hb_graph)
	If you only care about hbond networks, then you might not care about edges that have no incident edges. This function deletes those edges. More...

scoring::hbonds::graph::HBondGraphOP	hbond_graph_from_partial_rotsets (pose::Pose const &pose_in, pack::rotamer_set::RotamerSets const &original_rotsets, scoring::ScoreFunctionOP const &scorefxn_sc, scoring::ScoreFunctionOP const &scorefxn_bb, pack::rotamer_set::RotamerSetsOP &complete_rotsets_out, utility::vector1< bool > &position_had_rotset, float minimum_hb_cut)
	Construct an HBondGraph from a partial rotsets (like you might see during packing) @detail BB-BB hbonds are only included for the first residue. This means that prolines are not handled correctly. If proline is the first resdiue at a position and other residues are being packed at that position, any hbonds to the other Ns will not be reported. If one wishes to have BB-BB hbonds for all pairs, enable all 4 hbond terms for scorefxn_sc and leave scorefxn_bb as a nullptr (or a blank scorefxn) If your pose is symmetric, this internally desymmetrizes it and returns all hbonds. More...

scoring::hbonds::graph::HBondGraphOP	create_and_init_hbond_graph (rotamer_set::RotamerSets const &rotamer_sets)
	This combines the HBondGraph constructor and init_node_info(). The HBondGraph constructor can not take core.4 objects because it is in core.3 (as of the time this was written). More...

static basic::Tracer	TR ("core.pack.hbonds.HBondGraphInitializerIG")

Typedef Documentation

◆ HBondGraphInitializerIGCOP

using core::pack::hbonds::HBondGraphInitializerIGCOP = typedef utility::pointer::shared_ptr< HBondGraphInitializerIG const >

◆ HBondGraphInitializerIGOP

using core::pack::hbonds::HBondGraphInitializerIGOP = typedef utility::pointer::shared_ptr< HBondGraphInitializerIG >

Function Documentation

◆ create_and_init_hbond_graph()

scoring::hbonds::graph::HBondGraphOP core::pack::hbonds::create_and_init_hbond_graph ( rotamer_set::RotamerSets const & rotamer_sets )

inline

This combines the HBondGraph constructor and init_node_info(). The HBondGraph constructor can not take core.4 objects because it is in core.3 (as of the time this was written).

References init_node_info(), and core::pack::rotamer_set::RotamerSets::nrotamers().

Referenced by create_init_and_create_edges_for_hbond_graph().

◆ create_init_and_create_edges_for_hbond_graph()

scoring::hbonds::graph::HBondGraphOP core::pack::hbonds::create_init_and_create_edges_for_hbond_graph	(	rotamer_set::RotamerSetsOP	rotamer_sets,
		scoring::ScoreFunction const &	sfxn,
		pose::Pose const &	pose,
		Real	hydrogen_bond_threshold,
		Real	clash_threshold,
		Real	hbond_energy_threshold_for_satisfaction,
		bool	include_backbone_at_atom_level
	)

Construct atom level hbond graph, initialize the node information, score rotamers to create hbonds. This will not work perfectly if you are using symmetry because it does not score one-body interactions, but can still provide a good template.

References create_and_init_hbond_graph(), core::pack::create_packer_graph(), determine_atom_level_edge_info_for_all_edges(), determine_atom_level_node_info_for_all_nodes(), core::pose::Pose::energies(), core::scoring::hbonds::HBondDatabase::get_database(), core::pose::Pose::size(), and core::scoring::Energies::tenA_neighbor_graph().

Referenced by hbond_graph_from_partial_rotsets().

◆ delete_edges_with_degree_zero()

void core::pack::hbonds::delete_edges_with_degree_zero ( scoring::hbonds::graph::HBondGraph & hb_graph )

If you only care about hbond networks, then you might not care about edges that have no incident edges. This function deletes those edges.

References core::sequence::end.

◆ determine_atom_level_edge_info()

void core::pack::hbonds::determine_atom_level_edge_info	(	HBondEdge &	hb_edge,
		rotamer_set::RotamerSets const &	rotamer_sets,
		scoring::hbonds::HBondDatabase const &	database,
		utility::graph::Graph const &	tenA_neighbor_graph,
		pose::Pose const &	pose,
		Real	hbond_energy_threshold_for_satisfaction,
		conformation::symmetry::SymmetryInfoCOP	symm_info
	)

Add information regarding the atoms participating in hbonds (see find_hbonds_in_residue_pair() ). symm_info needs to be != 0 if and only if you want to evaluate symmetry.

References core::conformation::Residue::atom_base(), core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), find_hbonds_in_residue_pair(), core::scoring::hbond, core::scoring::hbonds::graph::HBondEdge::register_hbond(), core::pack::rotamer_set::RotamerSets::rotamer(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), and core::conformation::Residue::seqpos().

Referenced by determine_atom_level_edge_info_for_all_edges(), and protocols::hbnet::HBNet::MC_traverse_IG().

◆ determine_atom_level_edge_info_for_all_edges()

void core::pack::hbonds::determine_atom_level_edge_info_for_all_edges	(	scoring::hbonds::graph::HBondGraph &	hb_graph,
		rotamer_set::RotamerSets const &	rotamer_sets,
		scoring::hbonds::HBondDatabase const &	database,
		utility::graph::Graph const &	tenA_neighbor_graph,
		pose::Pose const &	pose,
		bool	skip_edges_with_degree_zero,
		Real	hbond_energy_threshold_for_satisfaction,
		conformation::symmetry::SymmetryInfoCOP	symm_info
	)

Iterate through edges and calls determine_atom_level_edge_info(). skip_edges_with_degree_zero does not evaluate edges that have no incident edges and can not be part of a hydrogen bond network. symm_info needs to be != 0 if and only if you want to evaluate symmetry.

References determine_atom_level_edge_info().

Referenced by create_init_and_create_edges_for_hbond_graph().

◆ determine_atom_level_node_info()

void core::pack::hbonds::determine_atom_level_node_info	(	HBondNode &	al_node,
		rotamer_set::RotamerSets const &	rotamer_sets,
		utility::vector1< bool > const &	include_these_resids,
		bool	include_backbone
	)

Store atom information for every node with a corresponding resid set to true in include_these_resids. include_these_resids was originally meant to protray "resid_is_buried" so that we only store atom info for buried residues. I don't care what you use this for so I gave it a more generalized name.

References core::scoring::hbonds::graph::HBondNode::add_polar_atom(), core::scoring::hbonds::graph::HBondNode::global_rotamer_id(), core::pack::rotamer_set::RotamerSets::moltenres_2_resid(), core::pack::rotamer_set::RotamerSets::moltenres_for_rotamer(), rot(), and core::pack::rotamer_set::RotamerSets::rotamer().

Referenced by determine_atom_level_node_info_for_all_nodes(), and protocols::hbnet::HBNet::MC_traverse_IG().

◆ determine_atom_level_node_info_for_all_nodes()

void core::pack::hbonds::determine_atom_level_node_info_for_all_nodes	(	scoring::hbonds::graph::HBondGraph &	hb_graph,
		rotamer_set::RotamerSets const &	rotamer_sets,
		utility::vector1< bool > const &	include_these_resids,
		bool	skip_nodes_with_no_edges,
		bool	include_backbone
	)

Calls determine_atom_level_node_info() for all nodes. skip_nodes_with_no_edges is recommended to be set to true but depends on your protocol. The default is false for safety purposes.

References determine_atom_level_node_info().

Referenced by create_init_and_create_edges_for_hbond_graph().

◆ find_hbonds_in_residue_pair()

void core::pack::hbonds::find_hbonds_in_residue_pair	(	conformation::Residue const &	resA,
		conformation::Residue const &	resB,
		scoring::hbonds::HBondDatabase const &	database,
		utility::graph::Graph const &	tenA_neighbor_graph,
		scoring::hbonds::HBondSet &	set
	)

Utility function used by other functions in this file. Given that an edge exists between two nodes, find all of the hbonds between those two residues. It does not matter which order resA and resB are. Output hbonds are put in the HBondSet provided. This should not be called before the graph is populated with edges (see HBondGraphInitializerIG) - nothing will crash if this is called with no edges but it just does not make sense.

References core::scoring::hbonds::identify_hbonds_1way(), and core::conformation::Residue::seqpos().

Referenced by determine_atom_level_edge_info(), and find_satisfying_interactions_with_background().

◆ find_satisfying_interactions_with_background()

void core::pack::hbonds::find_satisfying_interactions_with_background	(	HBondNode &	node,
		rotamer_set::RotamerSets const &	rotamer_sets,
		utility::graph::Graph const &	packer_neighbor_graph,
		pose::Pose const &	poly_ala_pose,
		Real	hbond_energy_threshold_for_satisfaction
	)

CALL determine_atom_level_node_info() OR determine_atom_level_node_info_for_all_nodes() BEFORE CALLING THIS! After adding atom info to nodes, calling this function will result in removing atom info for atoms that hydrogen bond with the backbone or fixed sidechains.

References core::sequence::end, core::pose::Pose::energies(), find_hbonds_in_residue_pair(), core::scoring::hbonds::HBondDatabase::get_database(), core::scoring::hbonds::graph::HBondNode::global_rotamer_id(), core::scoring::hbond, core::scoring::hbonds::graph::HBondNode::moltenres(), core::pack::rotamer_set::RotamerSets::moltenres_2_resid(), core::scoring::hbonds::graph::HBondNode::remove_atom_info(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer(), and core::scoring::Energies::tenA_neighbor_graph().

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

◆ get_symm_ind_res()

Size core::pack::hbonds::get_symm_ind_res	(	pose::Pose const &	pose,
		Size const	resid,
		conformation::symmetry::SymmetryInfoCOP	symm_info,
		std::map< char, std::pair< Size, Size > >	chain_bounds
	)

References core::pose::Pose::chain().

◆ hbond_graph_from_partial_rotsets()

scoring::hbonds::graph::HBondGraphOP core::pack::hbonds::hbond_graph_from_partial_rotsets	(	pose::Pose const &	pose_in,
		pack::rotamer_set::RotamerSets const &	original_rotsets,
		scoring::ScoreFunctionOP const &	scorefxn_sc,
		scoring::ScoreFunctionOP const &	scorefxn_bb,
		pack::rotamer_set::RotamerSetsOP &	complete_rotsets_out,
		utility::vector1< bool > &	position_had_rotset,
		float	minimum_hb_cut
	)

Construct an HBondGraph from a partial rotsets (like you might see during packing) @detail BB-BB hbonds are only included for the first residue. This means that prolines are not handled correctly. If proline is the first resdiue at a position and other residues are being packed at that position, any hbonds to the other Ns will not be reported. If one wishes to have BB-BB hbonds for all pairs, enable all 4 hbond terms for scorefxn_sc and leave scorefxn_bb as a nullptr (or a blank scorefxn) If your pose is symmetric, this internally desymmetrizes it and returns all hbonds.

Construct an HBondGraph from a partial rotsets (like you might see during packing) @detail BB-BB hbonds are only included for the first residue. This means that prolines are not handled correctly. If proline is the first resdiue at a position and other residues are being packed at that position, any hbonds to the other Ns will not be reported. If one wishes to have BB-BB hbonds for all pairs, enable all 4 hbond terms for scorefxn_sc and leave scorefxn_bb as a nullptr (or a blank scorefxn)

References core::pose::Pose::conformation(), create_init_and_create_edges_for_hbond_graph(), core::pack::task::TaskFactory::create_packer_task(), core::conformation::Residue::create_rotamer(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_asymmetric_pose(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), core::pose::Pose::size(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), and core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation().

◆ init_node_info()

void core::pack::hbonds::init_node_info	(	HBondGraph &	graph,
		rotamer_set::RotamerSets const &	rotamer_sets
	)

This should be called immediately after creating the graph (and setting the number of nodes if need-be). This adds rotamer_sets info to the nodes for easier lookup later. Technically optional but recommended.

References core::pack::rotamer_set::RotamerSets::moltenres_for_rotamer(), core::pack::rotamer_set::RotamerSets::nrotamers(), rot(), core::pack::rotamer_set::RotamerSets::rotid_on_moltenresidue(), core::scoring::hbonds::graph::HBondNode::set_local_rotamer_id(), and core::scoring::hbonds::graph::HBondNode::set_moltenres().

Referenced by create_and_init_hbond_graph(), and protocols::hbnet::HBNet::initialize_hbond_graph().

◆ TR()

static basic::Tracer core::pack::hbonds::TR ( "core.pack.hbonds.HBondGraphInitializerIG" )

static

Classes

Typedefs

Functions

Typedef Documentation

◆ HBondGraphInitializerIGCOP

◆ HBondGraphInitializerIGOP

Function Documentation

◆ create_and_init_hbond_graph()

◆ create_init_and_create_edges_for_hbond_graph()

◆ delete_edges_with_degree_zero()

◆ determine_atom_level_edge_info()

◆ determine_atom_level_edge_info_for_all_edges()

◆ determine_atom_level_node_info()

◆ determine_atom_level_node_info_for_all_nodes()

◆ find_hbonds_in_residue_pair()

◆ find_satisfying_interactions_with_background()

◆ get_symm_ind_res()

◆ hbond_graph_from_partial_rotsets()

◆ init_node_info()

◆ TR()