#include <HBNet.hh>

Inheritance diagram for protocols::hbnet::HBNet:

[legend]

Public Member Functions
	HBNet ()

	HBNet (std::string const name)

	HBNet (core::scoring::ScoreFunctionCOP scorefxn, core::Size max_unsat, core::Size min_network_size=3, core::Real hb_threshold=-0.75, core::Size max_network_size=15, std::string des_residues="STRKHYWNQDE", bool find_native=false, bool only_native=false, bool keep_existing=false, bool extend_existing=false, bool only_extend=false)

	~HBNet () override

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

virtual void	setup_packer_task_and_starting_residues (core::pose::Pose const &pose)

virtual void	trim_additional_rotamers (core::pose::Pose &)

virtual void	search_IG_for_networks (core::pose::Pose &pose)

virtual void	prepare_output ()

virtual bool	network_meets_initial_criteria (HBondNetStruct const &)
	initial criteria for screening that just reuqires HBondNetStruct (no scoring or placement of rotamers on the pose) More...

virtual bool	network_meets_final_criteria (core::pose::Pose const &, HBondNetStruct &)
	final criteria that reuqires network rotamers placed on pose More...

virtual bool	state_is_starting_aa_type (core::Size const, core::Size const)

virtual bool	pair_meets_starting_criteria (core::Size const, core::Size const, core::Size const, core::Size const)

core::Real	upweight_starting_twobody_energy ()

virtual core::Real	scale_twobody_energy (core::Real input_twobody_energy, char, char)

virtual std::string	print_additional_info_for_net (HBondNetStruct &, core::pose::Pose const &)

virtual std::string	print_additional_headers ()

virtual core::Size	ligand ()

bool	symmetric () const

void	symmetric (bool const is_symmetric_pose)

core::conformation::symmetry::SymmetryInfoCOP	get_symm_info () const

void	set_symm_info (core::conformation::symmetry::SymmetryInfoCOP const &symminfo)

bool	multi_component () const

void	multi_component (bool const multi_component)

bool	verbose () const

void	verbose (bool const set_verbose)

bool	pdb_numbering () const

void	pdb_numbering (bool const pdb_numbering)

std::set< core::Size >	get_start_res_vec ()

void	add_start_res (core::Size res)

void	set_start_res_vec (std::set< core::Size > const start_resnums)

void	set_start_resnums (std::set< core::Size > const start_resnums)

core::pack::task::PackerTaskOP	get_task () const

void	set_task (core::pack::task::PackerTaskOP const &task)

void	task_factory (core::pack::task::TaskFactoryOP const &task_factory)

core::pack::task::TaskFactoryOP	task_factory () const

void	set_core_residues (core::select::residue_selector::ResidueSubset core_residues)

core::select::residue_selector::ResidueSubset	get_core_residues ()

core::select::residue_selector::ResidueSelectorOP	get_core_selector ()

void	set_boundary_residues (core::select::residue_selector::ResidueSubset boundary_residues)

core::select::residue_selector::ResidueSubset	get_boundary_residues ()

core::select::residue_selector::ResidueSelectorOP	get_boundary_selector ()

void	update_core_and_boundary_residues (core::pose::Pose const &pose)

void	set_upweight_starting_twobody (core::Real upweight_factor)

std::vector< HBondNetStructOP > &	get_net_vec ()
	return all hbond networks, sorted with best networks at the front, THIS SHOULD RETURN A POINTER (OP) More...

std::vector< HBondNetStructOP > &	get_native_vec ()

std::vector< std::set< core::Size > > &	get_output_vector ()

HBondNetStructOP	get_network_by_id (core::Size id)

core::pose::Pose const &	get_orig_pose ()

void	set_orig_pose (core::pose::Pose &pose)

core::pose::Pose const &	get_ala_pose ()

void	set_ala_pose (core::pose::Pose &pose)

char	get_aa_for_state (core::Size const res, core::Size const rot) const

bool	res_is_boundary (core::Size const res) const

bool	res_is_core (core::Size const res) const

void	set_min_networks_size (core::Size min)

void	set_max_networks_size (core::Size max)

void	set_max_unsat (core::Size max)

core::Size	get_min_networks_size ()

core::Size	get_max_networks_size ()

core::Size	get_max_unsat ()

void	set_find_native (bool native)

bool	find_native ()

void	set_find_only_native (bool only)

bool	only_native ()

void	set_keep_existing_networks (bool keep_existing_networks)

bool	get_keep_existing_networks ()

void	set_extend_existing_networks (bool extend_existing_networks)

bool	get_extend_existing_networks ()

void	set_only_extend_existing (bool only_extend_existing)

bool	get_only_extend_existing ()

utility::graph::GraphOP	get_packer_graph ()

core::Size	num_core_res (HBondNetStruct const &network)

core::Size	num_boundary_res (HBondNetStruct const &network)

void	select_best_networks ()

std::vector< HBondNetStructOP >	get_networks ()

void	set_score_function (core::scoring::ScoreFunctionCOP const &sf)

bool	net_clash (HBondNetStruct const &i, HBondNetStruct const &j)
	checks if two h-bond networks clash; returns true if they do clash More...

void	set_symmetry (core::pose::Pose &pose)

core::Size	get_ind_res (core::pose::Pose const &pose, core::Size const res_i)

bool	quick_and_dirty_network_has_heavy_atom_unsat (core::pose::Pose const &pose, HBondNetStruct const &network)

bool	quick_and_dirty_heavy_atom_is_unsat (core::pose::Pose const &pose, core::id::AtomID const at_id)

bool	atom_hbonds_to_bridging_water (core::pose::Pose const &pose, core::id::AtomID const at_id)

void	find_unsats (core::pose::Pose const &pose, HBondNetStruct &i)

utility::vector1< core::Size >	place_rots_on_pose (core::pose::Pose &pose, HBondNetStruct &residues, bool use_pose=false)
	places the rotamers of the provided h-bond network onto the provided pose More...

core::Size	get_num_native_rot (core::pose::Pose &pose, utility::vector1< HBondResStructCOP > const &residues, core::Real sc_rmsd_cut=0.25, bool super=true)
	return the number of rotamers in a network that are identical in seq or rot to the original input pose: More...

core::Size	get_num_native_seq (core::pose::Pose &pose, utility::vector1< HBondResStructCOP > const &residues)

bool	water_clashes (core::pose::Pose const &pose, core::Vector const water_O)

bool	water_oxygen_clashes_with_residue (core::Vector const water_oxygen, core::Size const resnum, int const rot_state)

bool	water_oxygen_clashes_with_residue (core::Vector const water_oxygen, core::conformation::Residue const &res)

core::pose::PoseOP	get_additional_output () override
	used by the job distributor and MultiplePoseMover (MPM) to return poses OTF as requested (without need to store in memory) More...

std::string	get_file_name (core::Size id, std::string prefix, std::string extension)

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

void	set_monte_carlo_branch (bool setting)
	turn on or off the monte carlo branching protocol More...

void	set_total_num_mc_runs (core::Size setting)
	set number of monte carlo runs to be divided over all the seed hbonds. A single monte carlo run appears to take roughly 1 ms (very loose estimate). More...

void	set_monte_carlo_seed_threshold (core::Real setting)
	Maybe you only want to branch from strong hbonds. If this value is -1.2, then only hbonds with a strength of -1.2 or lower will be branched from. More...

void	set_monte_carlo_seed_must_be_buried (bool setting)
	Only branch from hbonds where at least one residue is buried. Effectively, this results in only finding networks that have at least one buried residue. More...

void	set_monte_carlo_seed_must_be_fully_buried (bool setting)
	Only branch from hbonds where both residues are buried. This results in only finding networks that have at least one buried hbond but this does not prevent having additional exposed hbonds. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Static Public Member Functions
static std::string	mover_name ()

static void	attributes_for_hbnet (utility::tag::AttributeList &)

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions
void	setup (core::pose::Pose const &pose)
	sets up rotamer_sets and makes preparations for populating the IG based on task_ops More...

void	get_native_networks (core::pose::Pose const &pose)

void	run (core::pose::Pose &pose)
	run common steps universal to all HBNet, e.g. finalize rotamer sets and scoring then populate and search IG for networks. More...

void	trim_rotamers (core::pose::Pose &pose)
	remove unwanted rotamers from rotamer_sets_ before IG is populated and searched. calls virtual trim_additional_rotamers() that can be overriden by specialized HBNet classes to remove additional rotmaers More...

void	traverse_native (core::pose::Pose const &pose, core::Real const hb_threshold)
	Do a recursive traversal of an EnergyGraph of a static pose; will find and store all native h-bond networks, regardless of score/parameters. More...

void	rec_trav_native (core::pose::Pose const &pose, core::Size new_res, core::Size prev_res, utility::vector1< HBondResStructCOP > residues, core::Real const hb_threshold)

void	traverse_IG (core::Real const hb_threshold)
	Recursively traverse the Interaction Graph ig_, and find all possible h-bond networks, given the parameters that have been set. More...

void	recursive_traverse (int const new_node_ind, int const newstate, core::Size const newres, core::Size const prevres, utility::vector1< HBondResStructCOP > residues, core::Size network_rec_count, core::Real init_sc, core::Real const hb_threshold, bool const second_search=false)

void	MC_traverse_IG ()
	A monte carlo alternative to traverse_IG() and recursive_traverse(). Basically just populates hbond_graph_. More...

bool	network_already_stored (utility::vector1< HBondResStructCOP > &residues, utility::vector1< HBondResStructCOP > &i_residues)
	@breif for efficiency, makes sure that an equivalent network has not already been stored More...

void	store_network (utility::vector1< HBondResStructCOP > residues, core::Real init_score=0.0, bool term_w_start=false, bool term_w_cycle=false, bool score_now=false, bool native=false)

void	score_network_on_pose (core::pose::Pose &pose, HBondNetStruct &i)
	void score_networks( bool minimize=false); More...

void	minimize_network (core::pose::Pose &pose, HBondNetStruct &network, bool residues_already_placed=true)

bool	check_clash (utility::vector1< HBondResStructCOP > const &residues, platform::uint my_node_ind, core::Size mystate, core::Size myres, core::Real &init_score, bool &cycle)
	check if a residue clashes with other reisdues in the network before adding it to the h-bond network. true = clashes More...

bool	net_clash (utility::vector1< HBondResStructCOP > const &residues_i, utility::vector1< HBondResStructCOP > const &residues_j)
	used by net_clash( HBondNetStruct & i, HBondNetStruct & j ), should not be called externally! More...

bool	monte_carlo_net_clash (utility::vector1< HBondResStructCOP > const &residues_i, utility::vector1< HBondResStructCOP > const &residues_j) const
	monte carlo protocol needs to use a different net_clash call because its IG is not populated More...

void	branch_overlapping_networks ()
	This function finds all networks that share a common rotamer, and then for ones that do not clash, branches them together in all possible combination to find all possible networks. More...

void	rec_set_intersection (std::vector< core::Size > add_index_vec, std::vector< core::Size > next_index_list, core::Size pos)
	used by branch_overlapping() to efficiently search for all combinations of compatible networks that can be merged More...

void	MC_branch_overlapping_networks ()
	monte carlo alternative to branch_overlapping_networks(). Requires MC_traverse_IG() to be called ahead of time. Theoretically O( total_num_mc_runs_ ) More...

void	merge_2_branched_networks (HBondNetStruct const &i, HBondNetStruct const &j, HBondNetStructOP new_network)
	Merges 2 networks (i,j) into a single h-bond network, new_network. More...

void	merge_2_branched_networks (utility::vector1< HBondResStructCOP > const &residues1, utility::vector1< HBondResStructCOP > const &residues2, utility::vector1< HBondResStructCOP > &new_residues)

bool	networks_unique (HBondNetStruct const &i, HBondNetStruct const &j, bool no_surface=true)

bool	networks_identical_aa_sequence (HBondNetStruct const &i, HBondNetStruct const &j)

bool	residues_identical (utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)

bool	residues_not_unique (utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)

bool	is_sub_residues (utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)
	Returns true if a network is a subset of another; it's symmetric, i.e. returns true if i is subset of j, or if j is a subset of i. More...

bool	is_sub_residues (utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2, bool &branch, bool true_if_identical=true)

void	remove_replicate_networks (core::Size same_max=1)
	Sorts all networks by score, removes replicate networks and networks > upper_score_limit; also removes subnetworks if store_subnetworks=false. More...

void	output_networks (bool finalize=false)
	Writes h-bond networks out to TR, and stores them in output_net_vec_ if finalize=true so they can be returned by get_additional_output(). More...

core::pack::task::PackerTaskOP	create_ptask (core::pose::Pose const &pose, bool initialize_from_commandline=false)

bool	task_is_valid (core::pose::Pose const &pose) const

bool	store_network_scores_in_pose () const

void	store_network_scores_in_pose (bool setting)

void	write_network_pdb (HBondNetStructOP &p)

void	set_constraints (core::pose::Pose &pose, core::scoring::constraints::ConstraintSet &constraints, HBondNetStruct &p, bool write_cst_file=false)

core::Size	chain_for_resid (core::Size resid) const

core::Size	chain_for_moltenres (core::Size mres) const

void	set_monte_carlo_data_to_default ()

void	initialize_hbond_graph ()
	This transfers rotamer sets data to hbond_graph_. Need to call this before traversing the IG. More...

void	register_clash (core::Size rotamerA, core::Size rotamerB)

virtual bool	edge_can_yield_monte_carlo_seed (core::Size resid1, core::Size resid2) const
	The edge_can_yield_monte_carlo_seed() methods determine if a hydrogen bond can be used as a seed for monte carlo branching. Examples of when this might fail include when the hbond does not cross the interface (for HBNetStapleInterface) or when the hbond is not buried to the level of the user's specifications. More...

virtual bool	edge_can_yield_monte_carlo_seed (core::pack::interaction_graph::EdgeBase const *) const

core::scoring::hbonds::graph::HBondNode *	get_next_node (NetworkState &current_state)
	get_next_node() randomly decides how the current_state will grow during the monte carlo branching protocol More...

bool	monte_carlo_seed_is_dead_end (core::scoring::hbonds::graph::HBondEdge const *monte_carlo_seed)
	returns true if this hbond can not create a network More...

void	append_to_network_vector (utility::vector1< DecoratedNetworkState > const &designed_networks)
	called at the end of the monte carlo branching protocol. Adds all of the monte carlo networks to the data elements used by the traditional HBNet protocol More...

void	add_residue_to_network_state (NetworkState &current_state, core::scoring::hbonds::graph::HBondNode *node_being_added) const

bool	network_state_is_satisfied (NetworkState &current_state) const
	quick and dirty satisfaction check More...

void	score_network_state (NetworkState &state) const
	evaluates state and stores the score in state.score More...

bool	register_new_network (NetworkState &current_network_state, utility::vector0< std::list< utility::vector1< core::Size > > > &hash_table, std::list< NetworkState > &designed_networks) const

bool	node_is_compatible (NetworkState const &current_state, core::scoring::hbonds::graph::HBondNode const *node_being_added)
	returns false if there is a clash between the node_being_added and any node currently in the current_state More...

bool	network_state_is_done_growing (NetworkState const &current_state, core::scoring::hbonds::graph::HBondGraphCOP hbond_graph)
	This is only being used for debug purposes right now. Makes sure that there are no possible nodes that can be added to current_state. More...

core::Real	estimate_saturation (NetworkState const &) const
	TODO. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Private Member Functions
core::pose::Pose &	nonconst_get_orig_pose ()

Private Attributes
bool	write_network_pdbs_

bool	write_cst_files_

bool	output_poly_ala_background_

bool	store_network_scores_in_pose_

bool	find_native_

bool	only_native_

bool	keep_existing_networks_

bool	extend_existing_networks_

bool	only_extend_existing_

bool	verbose_

bool	symmetric_

bool	multi_component_

bool	show_task_

bool	minimize_

bool	allow_no_hbnets_

bool	tyr_hydroxyls_must_donate_

bool	hydroxyls_must_donate_

bool	use_pdb_numbering_

bool	no_heavy_unsats_allowed_

bool	keep_start_selector_rotamers_fixed_

core::Size	min_network_size_

core::Size	max_network_size_

core::Size	min_unique_networks_

core::Size	min_core_res_

core::Size	min_boundary_res_

core::Size	max_unsat_Hpol_

core::Size	max_lig_unsat_

core::Size	max_rep_

core::Size	max_replicates_before_branch_

core::Size	max_replicates_before_unsat_check_

std::string const	allaas_

std::string const	hbond_default_

std::string const	hbond_disallow_default_

std::string	hbond_disallow_

std::string	des_residues_

std::set< core::Size >	start_res_vec_

std::vector< HBondNetStructOP >	network_vector_

std::vector< HBondNetStructOP >	native_networks_

std::vector< std::vector< core::Size > >	merged_vecs_

std::vector< std::set< core::Size > >	output_vector_

std::map< char, std::pair< core::Size, core::Size > >	chain_bounds_

core::Real	hydrogen_bond_threshold_

core::Real	onebody_hb_threshold_

core::Real	charge_charge_rep_cutoff_

core::PackerEnergy	clash_threshold_

core::Real	upper_score_limit_

core::Real	min_percent_hbond_capacity_

core::pose::PoseOP	ala_pose_

core::pose::PoseOP	orig_pose_

core::pack::task::PackerTaskOP	task_

core::pack::task::TaskFactoryOP	task_factory_

core::scoring::ScoreFunctionOP	init_scorefxn_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	bw_sfxn_

core::pack::rotamer_set::RotamerSetsOP	rotamer_sets_

core::pack::interaction_graph::InteractionGraphBaseOP	ig_

core::conformation::symmetry::SymmetryInfoCOP	symm_info_

core::pack::rotamer_set::RotamerLinksCOP	rotamer_links_

bool	store_subnetworks_

bool	secondary_search_

core::Real	secondary_threshold_

core::Real	upweight_twobody_

core::select::residue_selector::ResidueSelectorOP	start_selector_

core::select::residue_selector::ResidueSelectorOP	core_selector_

core::select::residue_selector::ResidueSelectorOP	boundary_selector_

core::select::residue_selector::ResidueSubset	core_residues_

core::select::residue_selector::ResidueSubset	boundary_residues_

core::select::residue_selector::ResidueSubset	input_hbnet_info_residues_

utility::graph::GraphOP	packer_neighbor_graph_

core::scoring::hbonds::HBondDatabaseCOP	hb_database_

bool	monte_carlo_branch_

core::Size	total_num_mc_runs_

core::Size	max_mc_nets_

core::scoring::hbonds::graph::HBondGraphOP	hbond_graph_

utility::vector1< core::scoring::hbonds::graph::HBondEdge const * >	monte_carlo_seeds_

core::Real	monte_carlo_seed_threshold_

bool	monte_carlo_seed_must_be_buried_

bool	monte_carlo_seed_must_be_fully_buried_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Constructor & Destructor Documentation

◆ HBNet() [1/3]

protocols::hbnet::HBNet::HBNet ( )

References set_monte_carlo_data_to_default().

◆ HBNet() [2/3]

protocols::hbnet::HBNet::HBNet ( std::string const name )

References set_monte_carlo_data_to_default().

◆ HBNet() [3/3]

protocols::hbnet::HBNet::HBNet	(	core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size	max_unsat,
		core::Size	min_network_size = `3`,
		core::Real	hb_threshold = `-0.75`,
		core::Size	max_network_size = `15`,
		std::string	des_residues = `"STRKHYWNQDE"`,
		bool	find_native = `false`,
		bool	only_native = `false`,
		bool	keep_existing = `false`,
		bool	extend_existing = `false`,
		bool	only_extend = `false`
	)

References extend_existing_networks_, find_native_, only_extend_existing_, only_native_, and set_monte_carlo_data_to_default().

◆ ~HBNet()

protocols::hbnet::HBNet::~HBNet ( )

overridedefault

Member Function Documentation

◆ add_residue_to_network_state()

void protocols::hbnet::HBNet::add_residue_to_network_state	(	NetworkState &	current_state,
		core::scoring::hbonds::graph::HBondNode *	node_being_added
	)		const

protected

References protocols::hbnet::NetworkState::add_polar_atoms(), protocols::hbnet::NetworkState::append_twobody_energy(), protocols::hbnet::NetworkState::edges(), core::scoring::hbonds::graph::HBondEdge::energy(), protocols::hbnet::NetworkState::full_twobody_energy(), protocols::hbnet::NetworkState::get_unsats_for_mres(), core::scoring::hbond, hbond_graph_, core::scoring::hbonds::graph::HBondEdge::hbonds(), core::scoring::hbonds::graph::HBondNode::moltenres(), protocols::hbnet::NetworkState::nodes(), core::scoring::hbonds::graph::AtomInfoSet::remove(), protocols::hbnet::NetworkState::score(), and symmetric_.

Referenced by MC_branch_overlapping_networks().

◆ add_start_res()

void protocols::hbnet::HBNet::add_start_res ( core::Size res )

inline

References start_res_vec_.

Referenced by protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ append_to_network_vector()

void protocols::hbnet::HBNet::append_to_network_vector ( utility::vector1< DecoratedNetworkState > const & designed_networks )

protected

called at the end of the monte carlo branching protocol. Adds all of the monte carlo networks to the data elements used by the traditional HBNet protocol

References chain_for_moltenres(), protocols::hbnet::NetworkState::edges(), get_net_vec(), max_mc_nets_, max_replicates_before_unsat_check_, protocols::hbnet::NetworkState::nodes(), rot(), rotamer_sets_, protocols::hbnet::NetworkState::score(), and task_.

Referenced by MC_branch_overlapping_networks().

◆ apply()

void protocols::hbnet::HBNet::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::add_comment(), ala_pose_, allow_no_hbnets_, boundary_residues_, boundary_selector_, clash_threshold_, protocols::membrane::com(), core::pose::Pose::constraint_set(), core_residues_, core_selector_, create_ptask(), core::pose::delete_comment(), des_residues_, extend_existing_networks_, protocols::moves::FAIL_RETRY, core::pose::get_all_comments(), get_network_by_id(), core::select::get_residue_set_from_subset(), core::scoring::get_score_function(), hydrogen_bond_threshold_, ig_, input_hbnet_info_residues_, core::pose::symmetry::is_symmetric(), keep_existing_networks_, monte_carlo_seeds_, protocols::moves::MS_SUCCESS, native_networks_, network_vector_, nonconst_get_orig_pose(), only_native_, orig_pose_, output_poly_ala_background_, output_vector_, packer_neighbor_graph_, core::pose::Pose::pdb_info(), place_rots_on_pose(), prepare_output(), print_additional_headers(), protocols::hbnet::print_headers(), res_is_core(), rotamer_links_, rotamer_sets_, run(), scorefxn_, set_constraints(), protocols::moves::Mover::set_last_move_status(), set_symmetry(), setup(), start_res_vec_, start_selector_, store_subnetworks_, task_factory_, core::pose::Pose::total_residue(), protocols::hbnet::TR(), core::pose::Pose::update_residue_neighbors(), verbose_, and write_cst_files_.

◆ atom_hbonds_to_bridging_water()

bool protocols::hbnet::HBNet::atom_hbonds_to_bridging_water	(	core::pose::Pose const &	pose,
		core::id::AtomID const	at_id
	)

References core::conformation::Residue::atom_is_polar_hydrogen(), core::conformation::Residue::atom_type(), core::id::AtomID::atomno(), core::chemical::AtomType::is_acceptor(), core::conformation::Residue::name1(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::pose::Pose::total_residue(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

◆ attributes_for_hbnet()

void protocols::hbnet::HBNet::attributes_for_hbnet ( utility::tag::AttributeList & attlist )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::scoring::attributes_for_parse_score_function(), and core::pack::task::attributes_for_parse_task_operations().

Referenced by provide_xml_schema(), and protocols::hbnet::HBNetStapleInterface::provide_xml_schema().

◆ branch_overlapping_networks()

void protocols::hbnet::HBNet::branch_overlapping_networks ( )

protected

This function finds all networks that share a common rotamer, and then for ones that do not clash, branches them together in all possible combination to find all possible networks.

Critical function to HBNet; because of depth-first traversal, need to combine networks for branched amino acids, e.g. ASN that can make multiple h-bonds The reason we need this is because bread-first additions ("branches") are order-dependent, meaning we need to try ALL combinations Branching is also a poor name as it is not "branching" in a computational or graph-theory sense

References is_sub_residues(), merge_2_branched_networks(), merged_vecs_, net_clash(), network_vector_, only_native_, protocols::hbnet::print_list_to_string(), rec_set_intersection(), store_subnetworks_, core::id::to_string(), protocols::hbnet::TR(), and verbose_.

Referenced by get_native_networks(), and run().

◆ chain_for_moltenres()

core::Size protocols::hbnet::HBNet::chain_for_moltenres ( core::Size mres ) const

inlineprotected

References chain_for_resid(), and rotamer_sets_.

Referenced by append_to_network_vector().

◆ chain_for_resid()

core::Size protocols::hbnet::HBNet::chain_for_resid ( core::Size resid ) const

inlineprotected

References orig_pose_.

Referenced by chain_for_moltenres(), and protocols::hbnet::HBNetStapleInterface::edge_can_yield_monte_carlo_seed().

◆ check_clash()

bool protocols::hbnet::HBNet::check_clash	(	utility::vector1< HBondResStructCOP > const &	residues,
		platform::uint	new_node_ind,
		core::Size	newstate,
		core::Size	newres,
		core::Real &	init_score,
		bool &	cycle
	)

protected

check if a residue clashes with other reisdues in the network before adding it to the h-bond network. true = clashes

Check if a new rotamer state clashes with any rotamer states already in a given h-bond network return of true = it clashes, false = no clashes

References clash_threshold_, core::pack::interaction_graph::EdgeBase::get_first_node_ind(), hydrogen_bond_threshold_, ig_, rotamer_sets_, symm_info_, and symmetric_.

Referenced by recursive_traverse().

◆ clone()

moves::MoverOP protocols::hbnet::HBNet::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::hbnet::HBNetStapleInterface.

◆ create_ptask()

core::pack::task::PackerTaskOP protocols::hbnet::HBNet::create_ptask	(	core::pose::Pose const &	pose,
		bool	initialize_from_commandline = `false`
	)

protected

References task_factory_, and protocols::hbnet::TR().

Referenced by apply(), setup_packer_task_and_starting_residues(), and protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ edge_can_yield_monte_carlo_seed() [1/2]

bool protocols::hbnet::HBNet::edge_can_yield_monte_carlo_seed ( core::pack::interaction_graph::EdgeBase const * edge ) const

protectedvirtual

References edge_can_yield_monte_carlo_seed(), core::pack::interaction_graph::EdgeBase::get_first_node_ind(), core::pack::interaction_graph::EdgeBase::get_second_node_ind(), and rotamer_sets_.

◆ edge_can_yield_monte_carlo_seed() [2/2]

bool protocols::hbnet::HBNet::edge_can_yield_monte_carlo_seed	(	core::Size	resid1,
		core::Size	resid2
	)		const

protectedvirtual

The edge_can_yield_monte_carlo_seed() methods determine if a hydrogen bond can be used as a seed for monte carlo branching. Examples of when this might fail include when the hbond does not cross the interface (for HBNetStapleInterface) or when the hbond is not buried to the level of the user's specifications.

Reimplemented in protocols::hbnet::HBNetStapleInterface.

References core_residues_, monte_carlo_seed_must_be_buried_, monte_carlo_seed_must_be_fully_buried_, and start_res_vec_.

Referenced by edge_can_yield_monte_carlo_seed(), protocols::hbnet::HBNetStapleInterface::edge_can_yield_monte_carlo_seed(), and MC_traverse_IG().

◆ estimate_saturation()

core::Real protocols::hbnet::HBNet::estimate_saturation ( NetworkState const & network_state ) const

protected

TODO.

References core::conformation::Residue::atom_type(), protocols::hbnet::NetworkState::edges(), core::chemical::AtomType::element(), core::sequence::end, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::conformation::Residue::Hpol_index(), core::chemical::AtomType::name(), core::conformation::Residue::nheavyatoms(), protocols::hbnet::NetworkState::nodes(), rotamer_sets_, and protocols::hbnet::TR().

Referenced by MC_branch_overlapping_networks().

◆ find_native()

bool protocols::hbnet::HBNet::find_native ( )

inline

References find_native_.

◆ find_unsats()

void protocols::hbnet::HBNet::find_unsats	(	core::pose::Pose const &	pose,
		HBondNetStruct &	i
	)

Referenced by get_native_networks(), output_networks(), and select_best_networks().

◆ fresh_instance()

moves::MoverOP protocols::hbnet::HBNet::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::hbnet::HBNetStapleInterface.

◆ get_aa_for_state()

char protocols::hbnet::HBNet::get_aa_for_state	(	core::Size const	res,
		core::Size const	rot
	)		const

References rot(), and rotamer_sets_.

Referenced by protocols::hbnet::HBNetStapleInterface::pair_meets_starting_criteria(), and protocols::hbnet::HBNetStapleInterface::state_is_starting_aa_type().

◆ get_additional_output()

pose::PoseOP protocols::hbnet::HBNet::get_additional_output ( )

overridevirtual

used by the job distributor and MultiplePoseMover (MPM) to return poses OTF as requested (without need to store in memory)

minimal h-bond network information is stored in memory and used here to place the rotamers onto a copy of input pose, returend on-the-fly as requested returns networks in order of ranking and automatically turns on constraints (added to Pose that's returned)

Reimplemented from protocols::moves::Mover.

References core::pose::add_comment(), ala_pose_, get_network_by_id(), orig_pose_, output_poly_ala_background_, output_vector_, place_rots_on_pose(), print_additional_headers(), protocols::hbnet::print_headers(), set_constraints(), protocols::hbnet::TR(), and write_cst_files_.

◆ get_ala_pose()

core::pose::Pose const& protocols::hbnet::HBNet::get_ala_pose ( )

inline

References ala_pose_.

◆ get_boundary_residues()

core::select::residue_selector::ResidueSubset protocols::hbnet::HBNet::get_boundary_residues ( )

inline

References boundary_residues_.

◆ get_boundary_selector()

core::select::residue_selector::ResidueSelectorOP protocols::hbnet::HBNet::get_boundary_selector ( )

inline

References boundary_selector_.

◆ get_core_residues()

core::select::residue_selector::ResidueSubset protocols::hbnet::HBNet::get_core_residues ( )

inline

References core_residues_.

◆ get_core_selector()

core::select::residue_selector::ResidueSelectorOP protocols::hbnet::HBNet::get_core_selector ( )

inline

References core_selector_.

◆ get_extend_existing_networks()

bool protocols::hbnet::HBNet::get_extend_existing_networks ( )

inline

References extend_existing_networks_.

Referenced by protocols::hbnet::HBNetStapleInterface::prepare_output().

◆ get_file_name()

std::string protocols::hbnet::HBNet::get_file_name	(	core::Size	id,
		std::string	prefix,
		std::string	extension
	)

References protocols::jd2::current_output_name(), and core::id::to_string().

Referenced by set_constraints(), and write_network_pdb().

◆ get_ind_res()

Size protocols::hbnet::HBNet::get_ind_res	(	core::pose::Pose const &	pose,
		core::Size const	res_i
	)

References core::pose::Pose::chain(), chain_bounds_, multi_component_, symm_info_, and symmetric_.

Referenced by rec_trav_native(), protocols::hbnet::HBNetStapleInterface::residues_are_interface_pairs(), protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(), traverse_IG(), and traverse_native().

◆ get_keep_existing_networks()

bool protocols::hbnet::HBNet::get_keep_existing_networks ( )

inline

References keep_existing_networks_.

Referenced by protocols::hbnet::HBNetStapleInterface::prepare_output().

◆ get_max_networks_size()

core::Size protocols::hbnet::HBNet::get_max_networks_size ( )

inline

References max_network_size_.

◆ get_max_unsat()

core::Size protocols::hbnet::HBNet::get_max_unsat ( )

inline

References max_unsat_Hpol_.

◆ get_min_networks_size()

core::Size protocols::hbnet::HBNet::get_min_networks_size ( )

inline

References min_network_size_.

◆ get_name()

std::string protocols::hbnet::HBNet::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Reimplemented in protocols::hbnet::HBNetStapleInterface.

References mover_name().

Referenced by provide_citation_info().

◆ get_native_networks()

void protocols::hbnet::HBNet::get_native_networks ( core::pose::Pose const & pose )

protected

◆ get_native_vec()

std::vector< HBondNetStructOP >& protocols::hbnet::HBNet::get_native_vec ( )

inline

References native_networks_.

Referenced by protocols::hbnet::HBNetStapleInterface::prepare_output().

◆ get_net_vec()

std::vector< HBondNetStructOP >& protocols::hbnet::HBNet::get_net_vec ( )

inline

return all hbond networks, sorted with best networks at the front, THIS SHOULD RETURN A POINTER (OP)

References network_vector_.

Referenced by append_to_network_vector(), protocols::hbnet::HBNetStapleInterface::prepare_output(), and protocols::hbnet::HBNetStapleInterface::rec_add_staple().

◆ get_network_by_id()

HBondNetStructOP protocols::hbnet::HBNet::get_network_by_id ( core::Size id )

inline

References network_vector_.

Referenced by apply(), get_additional_output(), output_networks(), protocols::hbnet::HBNetStapleInterface::prepare_output(), and protocols::hbnet::HBNetStapleInterface::rec_add_staple().

◆ get_networks()

std::vector< HBondNetStructOP > protocols::hbnet::HBNet::get_networks ( )

inline

References network_vector_.

◆ get_next_node()

HBondNode * protocols::hbnet::HBNet::get_next_node ( NetworkState & current_state )

protected

get_next_node() randomly decides how the current_state will grow during the monte carlo branching protocol

References protocols::hbnet::edge_satisfies_heavy_unsat_for_node(), core::scoring::hbonds::graph::HBondNode::global_rotamer_id(), hbond_graph_, protocols::hbnet::NetworkState::mres_has_heavy_unsats(), node_is_compatible(), protocols::hbnet::NetworkState::nodes(), core::scoring::rg, and protocols::hbnet::NetworkState::unsatisfied_sc_atoms_const().

Referenced by MC_branch_overlapping_networks().

◆ get_num_native_rot()

Size protocols::hbnet::HBNet::get_num_native_rot	(	core::pose::Pose &	pose,
		utility::vector1< HBondResStructCOP > const &	residues,
		core::Real	sc_rmsd_cut = `0.25`,
		bool	super = `true`
	)

return the number of rotamers in a network that are identical in seq or rot to the original input pose:

References core::conformation::Residue::clone(), ligand(), core::conformation::Residue::name1(), orig_pose_, core::pose::Pose::residue(), and core::scoring::residue_sc_rmsd_no_super().

◆ get_num_native_seq()

Size protocols::hbnet::HBNet::get_num_native_seq	(	core::pose::Pose &	pose,
		utility::vector1< HBondResStructCOP > const &	residues
	)

References ligand(), core::conformation::Residue::name1(), orig_pose_, and core::pose::Pose::residue().

◆ get_only_extend_existing()

bool protocols::hbnet::HBNet::get_only_extend_existing ( )

inline

References only_extend_existing_.

◆ get_orig_pose()

core::pose::Pose const& protocols::hbnet::HBNet::get_orig_pose ( )

inline

References orig_pose_.

Referenced by protocols::hbnet::HBNetStapleInterface::residues_are_interface_pairs().

◆ get_output_vector()

std::vector< std::set< core::Size > >& protocols::hbnet::HBNet::get_output_vector ( )

inline

References output_vector_.

Referenced by protocols::hbnet::HBNetStapleInterface::prepare_output(), and protocols::hbnet::HBNetStapleInterface::rec_add_staple().

◆ get_packer_graph()

utility::graph::GraphOP protocols::hbnet::HBNet::get_packer_graph ( )

inline

References packer_neighbor_graph_.

◆ get_start_res_vec()

std::set< core::Size > protocols::hbnet::HBNet::get_start_res_vec ( )

inline

References start_res_vec_.

Referenced by protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ get_symm_info()

core::conformation::symmetry::SymmetryInfoCOP protocols::hbnet::HBNet::get_symm_info ( ) const

inline

References symm_info_.

Referenced by protocols::hbnet::HBNetStapleInterface::has_pH_His(), and protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ get_task()

core::pack::task::PackerTaskOP protocols::hbnet::HBNet::get_task ( ) const

inline

References task_.

◆ initialize_hbond_graph()

void protocols::hbnet::HBNet::initialize_hbond_graph ( )

protected

This transfers rotamer sets data to hbond_graph_. Need to call this before traversing the IG.

References hbond_graph_, core::pack::hbonds::init_node_info(), and rotamer_sets_.

Referenced by run().

◆ is_sub_residues() [1/2]

bool protocols::hbnet::HBNet::is_sub_residues	(	utility::vector1< HBondResStructCOP > &	residues1,
		utility::vector1< HBondResStructCOP > &	residues2
	)

protected

Returns true if a network is a subset of another; it's symmetric, i.e. returns true if i is subset of j, or if j is a subset of i.

Referenced by branch_overlapping_networks(), output_networks(), protocols::hbnet::HBNetStapleInterface::rec_add_staple(), and remove_replicate_networks().

◆ is_sub_residues() [2/2]

bool protocols::hbnet::HBNet::is_sub_residues	(	utility::vector1< HBondResStructCOP > &	residues1,
		utility::vector1< HBondResStructCOP > &	residues2,
		bool &	branch,
		bool	true_if_identical = `true`
	)

protected

identical networks are considered subsets of each other here by default unless specified by true_if_identical=false std::includes() returns false if 2 vectors are identical

◆ ligand()

virtual core::Size protocols::hbnet::HBNet::ligand ( )

inlinevirtual

Referenced by get_num_native_rot(), get_num_native_seq(), merge_2_branched_networks(), minimize_network(), net_clash(), and store_network().

◆ MC_branch_overlapping_networks()

void protocols::hbnet::HBNet::MC_branch_overlapping_networks ( )

protected

monte carlo alternative to branch_overlapping_networks(). Requires MC_traverse_IG() to be called ahead of time. Theoretically O( total_num_mc_runs_ )

heart of MC-HBNet: use the MC seeds to stochastically grow networks to completion

References add_residue_to_network_state(), append_to_network_vector(), estimate_saturation(), get_next_node(), hbond_graph_, monte_carlo_seeds_, network_state_is_satisfied(), register_new_network(), core::scoring::rg, symmetric_, total_num_mc_runs_, and protocols::hbnet::TR().

Referenced by run().

◆ MC_traverse_IG()

void protocols::hbnet::HBNet::MC_traverse_IG ( )

protected

A monte carlo alternative to traverse_IG() and recursive_traverse(). Basically just populates hbond_graph_.

References ala_pose_, clash_threshold_, core_residues_, core::pack::hbonds::determine_atom_level_edge_info(), core::pack::hbonds::determine_atom_level_node_info(), edge_can_yield_monte_carlo_seed(), core::sequence::end, core::pack::hbonds::find_satisfying_interactions_with_background(), core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds(), core::scoring::hbonds::HBondDatabase::get_database(), hb_database_, hbond_graph_, ig_, core::scoring::hbonds::graph::HBondNode::local_rotamer_id(), core::scoring::hbonds::graph::HBondNode::moltenres(), monte_carlo_seed_is_dead_end(), monte_carlo_seed_threshold_, monte_carlo_seeds_, onebody_hb_threshold_, orig_pose_, packer_neighbor_graph_, pair_meets_starting_criteria(), protocols::jumping::rot1, protocols::jumping::rot2, rotamer_sets_, secondary_threshold_, symm_info_, and symmetric_.

Referenced by search_IG_for_networks().

◆ merge_2_branched_networks() [1/2]

void protocols::hbnet::HBNet::merge_2_branched_networks	(	HBondNetStruct const &	i,
		HBondNetStruct const &	j,
		HBondNetStructOP	new_network
	)

protected

Merges 2 networks (i,j) into a single h-bond network, new_network.

References protocols::hbnet::find_HBondResStruct(), protocols::hbnet::HBondNetStruct::is_extended, protocols::hbnet::HBondNetStruct::is_native, protocols::hbnet::HBondNetStruct::lig_state_list, ligand(), protocols::hbnet::HBondNetStruct::residues, protocols::hbnet::HBondNetStruct::term_w_bb, protocols::hbnet::HBondNetStruct::term_w_cycle, and protocols::hbnet::HBondNetStruct::term_w_start.

Referenced by branch_overlapping_networks().

◆ merge_2_branched_networks() [2/2]

void protocols::hbnet::HBNet::merge_2_branched_networks	(	utility::vector1< HBondResStructCOP > const &	residues1,
		utility::vector1< HBondResStructCOP > const &	residues2,
		utility::vector1< HBondResStructCOP > &	new_residues
	)

protected

◆ minimize_network()

void protocols::hbnet::HBNet::minimize_network	(	core::pose::Pose &	pose,
		HBondNetStruct &	network,
		bool	residues_already_placed = `true`
	)

protected

References core::conformation::Residue::clone(), protocols::hbnet::find_HBondResStruct(), protocols::hbnet::HBondNetStruct::is_native, ligand(), core::pose::symmetry::make_symmetric_movemap(), orig_pose_, place_rots_on_pose(), core::pose::Pose::residue(), protocols::hbnet::HBondNetStruct::residues, protocols::hbnet::HBondNetStruct::rotamers, scorefxn_, symm_info_, symmetric_, and core::pose::Pose::update_residue_neighbors().

Referenced by select_best_networks().

◆ monte_carlo_net_clash()

bool protocols::hbnet::HBNet::monte_carlo_net_clash	(	utility::vector1< HBondResStructCOP > const &	residues_i,
		utility::vector1< HBondResStructCOP > const &	residues_j
	)		const

protected

monte carlo protocol needs to use a different net_clash call because its IG is not populated

References core::scoring::hbonds::graph::HBondNode::clashes(), hbond_graph_, protocols::hbnet::one_network_is_subset_of_other(), core::scoring::residue_sc_rmsd_no_super(), protocols::jumping::rot1, protocols::jumping::rot2, rotamer_sets_, and protocols::hbnet::SC_RMSD_CUTOFF.

Referenced by net_clash().

◆ monte_carlo_seed_is_dead_end()

bool protocols::hbnet::HBNet::monte_carlo_seed_is_dead_end ( core::scoring::hbonds::graph::HBondEdge const * monte_carlo_seed )

protected

returns true if this hbond can not create a network

References core::scoring::hbonds::graph::HBondNode::clashes(), core::scoring::hbonds::graph::HBondNode::global_rotamer_id(), hbond_graph_, and core::scoring::hbonds::graph::HBondNode::moltenres().

Referenced by MC_traverse_IG().

◆ mover_name()

std::string protocols::hbnet::HBNet::mover_name ( )

static

Referenced by get_name(), protocols::hbnet::HBNetCreator::keyname(), and provide_xml_schema().

◆ multi_component() [1/2]

bool protocols::hbnet::HBNet::multi_component ( ) const

inline

References multi_component_.

Referenced by protocols::hbnet::HBNetStapleInterface::has_pH_His(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), and protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ multi_component() [2/2]

void protocols::hbnet::HBNet::multi_component ( bool const multi_component )

inline

References multi_component(), and multi_component_.

Referenced by multi_component().

◆ net_clash() [1/2]

bool protocols::hbnet::HBNet::net_clash	(	HBondNetStruct const &	i,
		HBondNetStruct const &	j
	)

checks if two h-bond networks clash; returns true if they do clash

Function to check whether two h-bond networks clash with eachother return of true = they clash, false = no clashes (networks i and j are compatible)

References protocols::hbnet::HBondNetStruct::residues.

Referenced by branch_overlapping_networks(), output_networks(), protocols::hbnet::HBNetStapleInterface::prepare_output(), and protocols::hbnet::HBNetStapleInterface::rec_add_staple().

◆ net_clash() [2/2]

bool protocols::hbnet::HBNet::net_clash	(	utility::vector1< HBondResStructCOP > const &	residues_i,
		utility::vector1< HBondResStructCOP > const &	residues_j
	)

protected

used by net_clash( HBondNetStruct & i, HBondNetStruct & j ), should not be called externally!

Function to check whether two h-bond networks clash with eachother return of true = they clash, false = no clashes (networks i and j are compatible)

References ala_pose_, clash_threshold_, core::scoring::fa_rep, core::pack::interaction_graph::EdgeBase::get_first_node_ind(), ig_, init_scorefxn_, ligand(), monte_carlo_branch_, monte_carlo_net_clash(), core::pose::Pose::replace_residue(), core::scoring::residue_sc_rmsd_no_super(), rotamer_sets_, protocols::hbnet::SC_RMSD_CUTOFF, symm_info_, and symmetric_.

◆ network_already_stored()

bool protocols::hbnet::HBNet::network_already_stored	(	utility::vector1< HBondResStructCOP > &	residues,
		utility::vector1< HBondResStructCOP > &	i_residues
	)

protected

@breif for efficiency, makes sure that an equivalent network has not already been stored

References core::scoring::residue_sc_rmsd_no_super(), protocols::jumping::rot1, protocols::jumping::rot2, rotamer_sets_, and protocols::hbnet::SC_RMSD_CUTOFF.

Referenced by store_network().

◆ network_meets_final_criteria()

virtual bool protocols::hbnet::HBNet::network_meets_final_criteria	(	core::pose::Pose const &	,
		HBondNetStruct &
	)

inlinevirtual

final criteria that reuqires network rotamers placed on pose

Reimplemented in protocols::hbnet::HBNetStapleInterface.

◆ network_meets_initial_criteria()

virtual bool protocols::hbnet::HBNet::network_meets_initial_criteria ( HBondNetStruct const & )

inlinevirtual

initial criteria for screening that just reuqires HBondNetStruct (no scoring or placement of rotamers on the pose)

Reimplemented in protocols::hbnet::HBNetStapleInterface.

Referenced by select_best_networks().

◆ network_state_is_done_growing()

bool protocols::hbnet::HBNet::network_state_is_done_growing	(	NetworkState const &	current_state,
		core::scoring::hbonds::graph::HBondGraphCOP	hbond_graph
	)

protected

This is only being used for debug purposes right now. Makes sure that there are no possible nodes that can be added to current_state.

References hbond_graph_, node_is_compatible(), and protocols::hbnet::NetworkState::nodes().

◆ network_state_is_satisfied()

bool protocols::hbnet::HBNet::network_state_is_satisfied ( NetworkState & current_state ) const

protected

quick and dirty satisfaction check

References protocols::hbnet::NetworkState::unsatisfied_sc_atoms_const().

Referenced by MC_branch_overlapping_networks().

◆ networks_identical_aa_sequence()

bool protocols::hbnet::HBNet::networks_identical_aa_sequence	(	HBondNetStruct const &	i,
		HBondNetStruct const &	j
	)

protected

References core::pose::motif::a(), and protocols::hbnet::HBondNetStruct::residues.

◆ networks_unique()

bool protocols::hbnet::HBNet::networks_unique	(	HBondNetStruct const &	i,
		HBondNetStruct const &	j,
		bool	no_surface = `true`
	)

protected

References res_is_boundary(), res_is_core(), protocols::hbnet::HBondNetStruct::residues, and residues_not_unique().

Referenced by select_best_networks().

◆ node_is_compatible()

bool protocols::hbnet::HBNet::node_is_compatible	(	NetworkState const &	current_state,
		core::scoring::hbonds::graph::HBondNode const *	node_being_added
	)

protected

returns false if there is a clash between the node_being_added and any node currently in the current_state

References core::scoring::hbonds::graph::HBondNode::clashes(), core::scoring::hbonds::graph::HBondNode::moltenres(), and protocols::hbnet::NetworkState::nodes().

Referenced by get_next_node(), and network_state_is_done_growing().

◆ nonconst_get_orig_pose()

core::pose::Pose& protocols::hbnet::HBNet::nonconst_get_orig_pose ( )

inlineprivate

References orig_pose_.

Referenced by apply().

◆ num_boundary_res()

Size protocols::hbnet::HBNet::num_boundary_res ( HBondNetStruct const & network )

References res_is_boundary(), and protocols::hbnet::HBondNetStruct::residues.

Referenced by select_best_networks().

◆ num_core_res()

Size protocols::hbnet::HBNet::num_core_res ( HBondNetStruct const & network )

References res_is_core(), and protocols::hbnet::HBondNetStruct::residues.

Referenced by select_best_networks().

◆ only_native()

bool protocols::hbnet::HBNet::only_native ( )

inline

References only_native_.

Referenced by protocols::hbnet::HBNetStapleInterface::prepare_output().

◆ output_networks()

void protocols::hbnet::HBNet::output_networks ( bool finalize = false )

protected

Writes h-bond networks out to TR, and stores them in output_net_vec_ if finalize=true so they can be returned by get_additional_output().

References core::pose::add_comment(), ala_pose_, core::pose::Pose::constraint_set(), extend_existing_networks_, find_native_, find_unsats(), protocols::hbnet::get_hbond_atom_pairs(), get_network_by_id(), is_sub_residues(), keep_existing_networks_, native_networks_, net_clash(), network_vector_, only_native_, orig_pose_, output_poly_ala_background_, output_vector_, pdb_numbering(), place_rots_on_pose(), print_additional_headers(), print_additional_info_for_net(), protocols::hbnet::print_headers(), protocols::hbnet::print_network(), protocols::hbnet::print_network_w_pdb_numbering(), score_network_on_pose(), set_constraints(), symmetric_, protocols::hbnet::TR(), write_cst_files_, write_network_pdb(), and write_network_pdbs_.

Referenced by prepare_output(), and protocols::hbnet::HBNetStapleInterface::prepare_output().

◆ pair_meets_starting_criteria()

virtual bool protocols::hbnet::HBNet::pair_meets_starting_criteria	(	core::Size const	,
		core::Size const	,
		core::Size const	,
		core::Size const
	)

inlinevirtual

Reimplemented in protocols::hbnet::HBNetStapleInterface.

Referenced by MC_traverse_IG(), and traverse_IG().

◆ parse_my_tag()

void protocols::hbnet::HBNet::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::hbnet::HBNetStapleInterface.

References allow_no_hbnets_, boundary_selector_, charge_charge_rep_cutoff_, clash_threshold_, core_selector_, des_residues_, protocols::pack_daemon::error_message, extend_existing_networks_, find_native_, core::select::residue_selector::get_residue_selector(), core::pose::get_resnum_selector(), hydrogen_bond_threshold_, hydroxyls_must_donate_, keep_existing_networks_, keep_start_selector_rotamers_fixed_, max_mc_nets_, max_network_size_, max_rep_, max_replicates_before_branch_, max_replicates_before_unsat_check_, max_unsat_Hpol_, min_boundary_res_, min_core_res_, min_network_size_, min_percent_hbond_capacity_, min_unique_networks_, minimize_, monte_carlo_branch_, monte_carlo_seed_must_be_buried_, monte_carlo_seed_must_be_fully_buried_, monte_carlo_seed_threshold_, no_heavy_unsats_allowed_, onebody_hb_threshold_, only_extend_existing_, only_native_, output_poly_ala_background_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), secondary_search_, secondary_threshold_, set_score_function(), show_task_, start_selector_, store_network_scores_in_pose_, store_subnetworks_, task_factory(), total_num_mc_runs_, protocols::hbnet::TR(), tyr_hydroxyls_must_donate_, upper_score_limit_, use_pdb_numbering_, verbose_, write_cst_files_, and write_network_pdbs_.

Referenced by protocols::hbnet::HBNetStapleInterface::parse_my_tag().

◆ pdb_numbering() [1/2]

bool protocols::hbnet::HBNet::pdb_numbering ( ) const

inline

References use_pdb_numbering_.

Referenced by output_networks().

◆ pdb_numbering() [2/2]

void protocols::hbnet::HBNet::pdb_numbering ( bool const pdb_numbering )

inline

References pdb_numbering(), and use_pdb_numbering_.

Referenced by pdb_numbering().

◆ place_rots_on_pose()

utility::vector1< core::Size > protocols::hbnet::HBNet::place_rots_on_pose	(	core::pose::Pose &	pose,
		HBondNetStruct &	residues,
		bool	use_pose = `false`
	)

◆ prepare_output()

void protocols::hbnet::HBNet::prepare_output ( )

virtual

Reimplemented in protocols::hbnet::HBNetStapleInterface.

References output_networks().

Referenced by apply().

◆ print_additional_headers()

virtual std::string protocols::hbnet::HBNet::print_additional_headers ( )

inlinevirtual

Reimplemented in protocols::hbnet::HBNetStapleInterface.

Referenced by apply(), get_additional_output(), output_networks(), set_constraints(), and write_network_pdb().

◆ print_additional_info_for_net()

virtual std::string protocols::hbnet::HBNet::print_additional_info_for_net	(	HBondNetStruct &	,
		core::pose::Pose const &
	)

inlinevirtual

Reimplemented in protocols::hbnet::HBNetStapleInterface.

Referenced by output_networks().

◆ provide_citation_info()

void protocols::hbnet::HBNet::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References get_name().

◆ provide_xml_schema()

void protocols::hbnet::HBNet::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References attributes_for_hbnet(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::hbnet::HBNetCreator::provide_xml_schema().

◆ quick_and_dirty_heavy_atom_is_unsat()

bool protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat	(	core::pose::Pose const &	pose,
		core::id::AtomID const	at_id
	)

References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), core::id::AtomID::atomno(), core::conformation::Residue::Hpos_polar(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::pose::Pose::total_residue(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

Referenced by quick_and_dirty_network_has_heavy_atom_unsat().

◆ quick_and_dirty_network_has_heavy_atom_unsat()

bool protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat	(	core::pose::Pose const &	pose,
		HBondNetStruct const &	network
	)

References core::conformation::Residue::accpt_pos_sc(), core::conformation::Residue::atom_base(), core::conformation::Residue::Hpos_polar_sc(), quick_and_dirty_heavy_atom_is_unsat(), res_is_core(), core::pose::Pose::residue(), and protocols::hbnet::HBondNetStruct::residues.

Referenced by select_best_networks().

◆ rec_set_intersection()

void protocols::hbnet::HBNet::rec_set_intersection	(	std::vector< core::Size >	add_index_vec,
		std::vector< core::Size >	next_index_list,
		core::Size	pos
	)

protected

used by branch_overlapping() to efficiently search for all combinations of compatible networks that can be merged

References merged_vecs_, network_vector_, and store_subnetworks_.

Referenced by branch_overlapping_networks().

◆ rec_trav_native()

void protocols::hbnet::HBNet::rec_trav_native	(	core::pose::Pose const &	pose,
		core::Size	new_res,
		core::Size	prev_res,
		utility::vector1< HBondResStructCOP >	residues,
		core::Real const	hb_threshold
	)

protected

References core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), get_ind_res(), core::scoring::hbond_sc, hydrogen_bond_threshold_, core::conformation::Residue::is_ligand(), core::conformation::Residue::is_protein(), core::conformation::Residue::name1(), orig_pose_, core::pose::Pose::residue(), store_network(), store_subnetworks_, and symmetric_.

Referenced by traverse_native().

◆ recursive_traverse()

void protocols::hbnet::HBNet::recursive_traverse	(	int const	new_node_ind,
		int const	newstate,
		core::Size const	newres,
		core::Size const	prevres,
		utility::vector1< HBondResStructCOP >	residues,
		core::Size	network_rec_count,
		core::Real	init_sc,
		core::Real const	hb_threshold,
		bool const	second_search = `false`
	)

protected

recursive call for depth-first traversal of IG

References check_clash(), clash_threshold_, ig_, max_network_size_, orig_pose_, rotamer_sets_, scale_twobody_energy(), secondary_search_, secondary_threshold_, start_res_vec_, store_network(), store_subnetworks_, symm_info_, and symmetric_.

Referenced by traverse_IG().

◆ register_clash()

void protocols::hbnet::HBNet::register_clash	(	core::Size	rotamerA,
		core::Size	rotamerB
	)

inlineprotected

References hbond_graph_.

◆ register_new_network()

bool protocols::hbnet::HBNet::register_new_network	(	NetworkState &	current_network_state,
		utility::vector0< std::list< utility::vector1< core::Size > > > &	hash_table,
		std::list< NetworkState > &	designed_networks
	)		const

protected

References protocols::hbnet::NetworkState::nodes(), score_network_state(), and core::simple_metrics::metrics::sum.

Referenced by MC_branch_overlapping_networks().

◆ remove_replicate_networks()

void protocols::hbnet::HBNet::remove_replicate_networks ( core::Size same_max = 1 )

protected

Sorts all networks by score, removes replicate networks and networks > upper_score_limit; also removes subnetworks if store_subnetworks=false.

References is_sub_residues(), network_vector_, only_native_, protocols::hbnet::print_list_to_string(), residues_identical(), protocols::hbnet::TR(), verbose(), and verbose_.

Referenced by get_native_networks(), and run().

◆ res_is_boundary()

bool protocols::hbnet::HBNet::res_is_boundary ( core::Size const res ) const

References boundary_residues_.

Referenced by networks_unique(), and num_boundary_res().

◆ res_is_core()

bool protocols::hbnet::HBNet::res_is_core ( core::Size const res ) const

References core_residues_.

Referenced by apply(), find_unsats(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), networks_unique(), num_core_res(), and quick_and_dirty_network_has_heavy_atom_unsat().

◆ residues_identical()

bool protocols::hbnet::HBNet::residues_identical	(	utility::vector1< HBondResStructCOP > &	residues1,
		utility::vector1< HBondResStructCOP > &	residues2
	)

protected

Referenced by remove_replicate_networks().

◆ residues_not_unique()

bool protocols::hbnet::HBNet::residues_not_unique	(	utility::vector1< HBondResStructCOP > &	residues1,
		utility::vector1< HBondResStructCOP > &	residues2
	)

protected

Referenced by networks_unique().

◆ run()

void protocols::hbnet::HBNet::run ( core::pose::Pose & pose )

protected

run common steps universal to all HBNet, e.g. finalize rotamer sets and scoring then populate and search IG for networks.

References branch_overlapping_networks(), clash_threshold_, core::pack::create_packer_graph(), protocols::hbnet::hbnet_symm_one_body_energies(), hbond_graph_, hydrogen_bond_threshold_, ig_, init_scorefxn_, initialize_hbond_graph(), max_rep_, max_replicates_before_branch_, max_replicates_before_unsat_check_, MC_branch_overlapping_networks(), monte_carlo_branch_, network_vector_, only_native_, packer_neighbor_graph_, remove_replicate_networks(), rotamer_sets_, search_IG_for_networks(), select_best_networks(), start_res_vec_, symmetric_, task_, protocols::hbnet::TR(), trim_rotamers(), and verbose_.

Referenced by apply().

◆ scale_twobody_energy()

virtual core::Real protocols::hbnet::HBNet::scale_twobody_energy	(	core::Real	input_twobody_energy,
		char	,
		char
	)

inlinevirtual

Reimplemented in protocols::hbnet::HBNetStapleInterface.

Referenced by recursive_traverse(), and traverse_IG().

◆ score_network_on_pose()

void protocols::hbnet::HBNet::score_network_on_pose	(	core::pose::Pose &	pose,
		HBondNetStruct &	i
	)

protected

void score_networks( bool minimize=false);

References ala_pose_, core::pose::Pose::energies(), core::scoring::EMapVector::get(), core::scoring::hbond_bb_sc, protocols::hbnet::MIN_HB_E_CUTOFF, protocols::hbnet::HBondNetStruct::residues, protocols::hbnet::HBondNetStruct::score, protocols::hbnet::HBondNetStruct::scored, symm_info_, symmetric_, protocols::hbnet::HBondNetStruct::term_w_bb, core::scoring::Energies::total_energies(), and core::scoring::total_score.

Referenced by get_native_networks(), output_networks(), and select_best_networks().

◆ score_network_state()

void protocols::hbnet::HBNet::score_network_state ( NetworkState & state ) const

protected

evaluates state and stores the score in state.score

References protocols::hbnet::NetworkState::full_twobody_energy(), protocols::hbnet::NetworkState::nodes(), and protocols::hbnet::NetworkState::score().

Referenced by register_new_network().

◆ search_IG_for_networks()

void protocols::hbnet::HBNet::search_IG_for_networks ( core::pose::Pose & pose )

virtual

References hydrogen_bond_threshold_, ig_, MC_traverse_IG(), monte_carlo_branch_, protocols::hbnet::TR(), and traverse_IG().

Referenced by run().

◆ select_best_networks()

void protocols::hbnet::HBNet::select_best_networks ( )

◆ set_ala_pose()

void protocols::hbnet::HBNet::set_ala_pose ( core::pose::Pose & pose )

inline

References ala_pose_.

◆ set_boundary_residues()

void protocols::hbnet::HBNet::set_boundary_residues ( core::select::residue_selector::ResidueSubset boundary_residues )

inline

References boundary_residues_.

◆ set_constraints()

void protocols::hbnet::HBNet::set_constraints	(	core::pose::Pose &	pose,
		core::scoring::constraints::ConstraintSet &	constraints,
		HBondNetStruct &	p,
		bool	write_cst_file = `false`
	)

protected

References core::pose::add_comment(), core::scoring::constraints::ConstraintSet::add_constraint(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), protocols::hbnet::HBondNetStruct::cst_file_written, get_file_name(), core::scoring::hbonds::hb_energy(), protocols::hbnet::HBondNetStruct::hbond_vec, protocols::hbnet::HBondNetStruct::id, core::conformation::membrane::in, protocols::hbnet::HBondNetStruct::is_extended, protocols::hbnet::HBondNetStruct::is_native, core::scoring::func::FuncFactory::new_func(), core::conformation::membrane::out, protocols::hbnet::HBondNetStruct::outstring, print_additional_headers(), protocols::hbnet::print_headers(), core::pose::Pose::residue(), core::id::to_string(), and core::conformation::Atom::xyz().

Referenced by apply(), get_additional_output(), output_networks(), and write_network_pdb().

◆ set_core_residues()

void protocols::hbnet::HBNet::set_core_residues ( core::select::residue_selector::ResidueSubset core_residues )

inline

References core_residues_.

◆ set_extend_existing_networks()

void protocols::hbnet::HBNet::set_extend_existing_networks ( bool extend_existing_networks )

inline

References extend_existing_networks_.

◆ set_find_native()

void protocols::hbnet::HBNet::set_find_native ( bool native )

inline

References find_native_.

◆ set_find_only_native()

void protocols::hbnet::HBNet::set_find_only_native ( bool only )

inline

References find_native_, and only_native_.

◆ set_keep_existing_networks()

void protocols::hbnet::HBNet::set_keep_existing_networks ( bool keep_existing_networks )

inline

References keep_existing_networks_.

◆ set_max_networks_size()

void protocols::hbnet::HBNet::set_max_networks_size ( core::Size max )

inline

References protocols::mean_field::max(), and max_network_size_.

◆ set_max_unsat()

void protocols::hbnet::HBNet::set_max_unsat ( core::Size max )

inline

References protocols::mean_field::max(), and max_unsat_Hpol_.

◆ set_min_networks_size()

void protocols::hbnet::HBNet::set_min_networks_size ( core::Size min )

inline

References protocols::mean_field::min(), and min_network_size_.

◆ set_monte_carlo_branch()

void protocols::hbnet::HBNet::set_monte_carlo_branch ( bool setting )

inline

turn on or off the monte carlo branching protocol

References monte_carlo_branch_.

◆ set_monte_carlo_data_to_default()

void protocols::hbnet::HBNet::set_monte_carlo_data_to_default ( )

inlineprotected

References max_mc_nets_, monte_carlo_branch_, monte_carlo_seed_must_be_buried_, monte_carlo_seed_must_be_fully_buried_, monte_carlo_seed_threshold_, monte_carlo_seeds_, and total_num_mc_runs_.

Referenced by HBNet().

◆ set_monte_carlo_seed_must_be_buried()

void protocols::hbnet::HBNet::set_monte_carlo_seed_must_be_buried ( bool setting )

inline

Only branch from hbonds where at least one residue is buried. Effectively, this results in only finding networks that have at least one buried residue.

References monte_carlo_seed_must_be_buried_.

◆ set_monte_carlo_seed_must_be_fully_buried()

void protocols::hbnet::HBNet::set_monte_carlo_seed_must_be_fully_buried ( bool setting )

inline

Only branch from hbonds where both residues are buried. This results in only finding networks that have at least one buried hbond but this does not prevent having additional exposed hbonds.

References monte_carlo_seed_must_be_fully_buried_.

◆ set_monte_carlo_seed_threshold()

void protocols::hbnet::HBNet::set_monte_carlo_seed_threshold ( core::Real setting )

inline

Maybe you only want to branch from strong hbonds. If this value is -1.2, then only hbonds with a strength of -1.2 or lower will be branched from.

References monte_carlo_seed_threshold_.

◆ set_only_extend_existing()

void protocols::hbnet::HBNet::set_only_extend_existing ( bool only_extend_existing )

inline

References extend_existing_networks_, and only_extend_existing_.

◆ set_orig_pose()

void protocols::hbnet::HBNet::set_orig_pose ( core::pose::Pose & pose )

inline

References orig_pose_.

◆ set_score_function()

void protocols::hbnet::HBNet::set_score_function ( core::scoring::ScoreFunctionCOP const & sf )

inline

References scorefxn_.

Referenced by parse_my_tag().

◆ set_start_res_vec()

void protocols::hbnet::HBNet::set_start_res_vec ( std::set< core::Size > const start_resnums )

inline

References start_res_vec_.

◆ set_start_resnums()

void protocols::hbnet::HBNet::set_start_resnums ( std::set< core::Size > const start_resnums )

inline

References start_res_vec_.

◆ set_symm_info()

void protocols::hbnet::HBNet::set_symm_info ( core::conformation::symmetry::SymmetryInfoCOP const & symminfo )

inline

References symm_info_.

◆ set_symmetry()

void protocols::hbnet::HBNet::set_symmetry ( core::pose::Pose & pose )

References core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), chain_bounds_, core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), multi_component_, core::pose::symmetry::sym_dof_names(), symm_info_, symmetric_, and protocols::hbnet::TR().

Referenced by apply().

◆ set_task()

void protocols::hbnet::HBNet::set_task ( core::pack::task::PackerTaskOP const & task )

inline

References task_.

Referenced by protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ set_total_num_mc_runs()

void protocols::hbnet::HBNet::set_total_num_mc_runs ( core::Size setting )

inline

set number of monte carlo runs to be divided over all the seed hbonds. A single monte carlo run appears to take roughly 1 ms (very loose estimate).

References total_num_mc_runs_.

◆ set_upweight_starting_twobody()

void protocols::hbnet::HBNet::set_upweight_starting_twobody ( core::Real upweight_factor )

inline

References upweight_twobody_.

Referenced by protocols::hbnet::HBNetStapleInterface::parse_my_tag().

◆ setup()

void protocols::hbnet::HBNet::setup ( core::pose::Pose const & pose )

protected

sets up rotamer_sets and makes preparations for populating the IG based on task_ops

References core::conformation::Residue::aa(), core::chemical::aa_vrt, ala_pose_, protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), des_residues_, extend_existing_networks_, find_native_, get_native_networks(), input_hbnet_info_residues_, core::conformation::Residue::is_protein(), keep_existing_networks_, keep_start_selector_rotamers_fixed_, native_networks_, only_extend_existing_, only_native_, core::pose::Pose::residue(), rotamer_links_, rotamer_sets_, setup_packer_task_and_starting_residues(), show_task_, start_res_vec_, symm_info_, symmetric_, task_, task_is_valid(), protocols::analysis::total, core::pose::Pose::total_residue(), and protocols::hbnet::TR().

Referenced by apply().

◆ setup_packer_task_and_starting_residues()

void protocols::hbnet::HBNet::setup_packer_task_and_starting_residues ( core::pose::Pose const & pose )

virtual

Reimplemented in protocols::hbnet::HBNetStapleInterface.

References create_ptask(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), start_res_vec_, task_, task_factory_, and core::pose::Pose::total_residue().

Referenced by setup().

◆ state_is_starting_aa_type()

virtual bool protocols::hbnet::HBNet::state_is_starting_aa_type	(	core::Size const	,
		core::Size const
	)

inlinevirtual

Reimplemented in protocols::hbnet::HBNetStapleInterface.

Referenced by traverse_IG().

◆ store_network()

void protocols::hbnet::HBNet::store_network	(	utility::vector1< HBondResStructCOP >	residues,
		core::Real	init_score = `0.0`,
		bool	term_w_start = `false`,
		bool	term_w_cycle = `false`,
		bool	score_now = `false`,
		bool	native = `false`
	)

protected

References ala_pose_, protocols::hbnet::find_HBondResStruct(), ligand(), network_already_stored(), network_vector_, and protocols::hybridization::score.

Referenced by rec_trav_native(), recursive_traverse(), and traverse_IG().

◆ store_network_scores_in_pose() [1/2]

bool protocols::hbnet::HBNet::store_network_scores_in_pose ( ) const

inlineprotected

References store_network_scores_in_pose_.

◆ store_network_scores_in_pose() [2/2]

void protocols::hbnet::HBNet::store_network_scores_in_pose ( bool setting )

inlineprotected

References store_network_scores_in_pose_.

◆ symmetric() [1/2]

bool protocols::hbnet::HBNet::symmetric ( ) const

inline

References symmetric_.

Referenced by protocols::hbnet::HBNetStapleInterface::edge_can_yield_monte_carlo_seed(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::hbnet::HBNetStapleInterface::network_meets_initial_criteria(), and protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ symmetric() [2/2]

void protocols::hbnet::HBNet::symmetric ( bool const is_symmetric_pose )

inline

References symmetric_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::hbnet::HBNet::task_factory ( ) const

inline

References task_factory_.

Referenced by parse_my_tag(), and protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ task_factory() [2/2]

void protocols::hbnet::HBNet::task_factory ( core::pack::task::TaskFactoryOP const & task_factory )

inline

References task_factory(), and task_factory_.

Referenced by task_factory().

◆ task_is_valid()

bool protocols::hbnet::HBNet::task_is_valid ( core::pose::Pose const & pose ) const

protected

References core::pose::Pose::residue_type_ptr(), task_, and core::pose::Pose::total_residue().

Referenced by setup().

◆ traverse_IG()

void protocols::hbnet::HBNet::traverse_IG ( core::Real const hb_threshold )

protected

Recursively traverse the Interaction Graph ig_, and find all possible h-bond networks, given the parameters that have been set.

Traverse IG to enumerate all possible h-bond networks; networks are stored using the store_networks() function and pushed to the back of network_vector_

References clash_threshold_, get_ind_res(), core::pack::interaction_graph::EdgeBase::get_other_ind(), ig_, onebody_hb_threshold_, orig_pose_, pair_meets_starting_criteria(), recursive_traverse(), rotamer_sets_, scale_twobody_energy(), start_res_vec_, state_is_starting_aa_type(), store_network(), symm_info_, symmetric_, and upweight_starting_twobody_energy().

Referenced by search_IG_for_networks().

◆ traverse_native()

void protocols::hbnet::HBNet::traverse_native	(	core::pose::Pose const &	pose,
		core::Real const	hb_threshold
	)

protected

Do a recursive traversal of an EnergyGraph of a static pose; will find and store all native h-bond networks, regardless of score/parameters.

traverse EnergyGraph of static pose to find all native networks

References core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), get_ind_res(), core::scoring::hbond_sc, hydrogen_bond_threshold_, core::conformation::Residue::is_ligand(), core::conformation::Residue::is_protein(), core::conformation::Residue::name1(), orig_pose_, rec_trav_native(), core::pose::Pose::residue(), start_res_vec_, and symmetric_.

Referenced by get_native_networks().

◆ trim_additional_rotamers()

virtual void protocols::hbnet::HBNet::trim_additional_rotamers ( core::pose::Pose & )

inlinevirtual

Referenced by trim_rotamers().

◆ trim_rotamers()

void protocols::hbnet::HBNet::trim_rotamers ( core::pose::Pose & pose )

protected

remove unwanted rotamers from rotamer_sets_ before IG is populated and searched. calls virtual trim_additional_rotamers() that can be overriden by specialized HBNet classes to remove additional rotmaers

References trim_additional_rotamers().

Referenced by run().

◆ update_core_and_boundary_residues()

void protocols::hbnet::HBNet::update_core_and_boundary_residues ( core::pose::Pose const & pose )

References core_residues_, and core_selector_.

◆ upweight_starting_twobody_energy()

core::Real protocols::hbnet::HBNet::upweight_starting_twobody_energy ( )

inline

References upweight_twobody_.

Referenced by traverse_IG().

◆ verbose() [1/2]

bool protocols::hbnet::HBNet::verbose ( ) const

inline

References verbose_.

Referenced by protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), remove_replicate_networks(), and protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues().

◆ verbose() [2/2]

void protocols::hbnet::HBNet::verbose ( bool const set_verbose )

inline

References verbose_.

◆ water_clashes()

bool protocols::hbnet::HBNet::water_clashes	(	core::pose::Pose const &	pose,
		core::Vector const	water_O
	)

References core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), symmetric_, core::pose::Pose::total_residue(), and water_oxygen_clashes_with_residue().

◆ water_oxygen_clashes_with_residue() [1/2]

bool protocols::hbnet::HBNet::water_oxygen_clashes_with_residue	(	core::Vector const	water_oxygen,
		core::conformation::Residue const &	res
	)

◆ water_oxygen_clashes_with_residue() [2/2]

bool protocols::hbnet::HBNet::water_oxygen_clashes_with_residue	(	core::Vector const	water_oxygen,
		core::Size const	resnum,
		int const	rot_state
	)

Referenced by water_clashes().

◆ write_network_pdb()

void protocols::hbnet::HBNet::write_network_pdb ( HBondNetStructOP & p )

protected

References core::pose::add_comment(), ala_pose_, core::pose::Pose::constraint_set(), protocols::jd2::current_output_name(), core::pose::Pose::dump_pdb(), get_file_name(), place_rots_on_pose(), print_additional_headers(), protocols::hbnet::print_headers(), and set_constraints().

Referenced by output_networks().

Member Data Documentation

◆ ala_pose_

core::pose::PoseOP protocols::hbnet::HBNet::ala_pose_

private

Referenced by apply(), get_additional_output(), get_ala_pose(), get_native_networks(), MC_traverse_IG(), net_clash(), output_networks(), score_network_on_pose(), select_best_networks(), set_ala_pose(), setup(), store_network(), and write_network_pdb().

◆ allaas_

std::string const protocols::hbnet::HBNet::allaas_

private

◆ allow_no_hbnets_

bool protocols::hbnet::HBNet::allow_no_hbnets_

private

Referenced by apply(), and parse_my_tag().

◆ boundary_residues_

core::select::residue_selector::ResidueSubset protocols::hbnet::HBNet::boundary_residues_

private

Referenced by apply(), get_boundary_residues(), res_is_boundary(), and set_boundary_residues().

◆ boundary_selector_

core::select::residue_selector::ResidueSelectorOP protocols::hbnet::HBNet::boundary_selector_

private

Referenced by apply(), get_boundary_selector(), and parse_my_tag().

◆ bw_sfxn_

core::scoring::ScoreFunctionOP protocols::hbnet::HBNet::bw_sfxn_

private

◆ chain_bounds_

std::map<char,std::pair<core::Size,core::Size> > protocols::hbnet::HBNet::chain_bounds_

private

Referenced by get_ind_res(), and set_symmetry().

◆ charge_charge_rep_cutoff_

core::Real protocols::hbnet::HBNet::charge_charge_rep_cutoff_

private

Referenced by parse_my_tag().

◆ clash_threshold_

core::PackerEnergy protocols::hbnet::HBNet::clash_threshold_

private

Referenced by apply(), check_clash(), MC_traverse_IG(), net_clash(), parse_my_tag(), recursive_traverse(), run(), and traverse_IG().

◆ core_residues_

core::select::residue_selector::ResidueSubset protocols::hbnet::HBNet::core_residues_

private

Referenced by apply(), edge_can_yield_monte_carlo_seed(), get_core_residues(), MC_traverse_IG(), res_is_core(), set_core_residues(), and update_core_and_boundary_residues().

◆ core_selector_

core::select::residue_selector::ResidueSelectorOP protocols::hbnet::HBNet::core_selector_

private

Referenced by apply(), get_core_selector(), parse_my_tag(), and update_core_and_boundary_residues().

◆ des_residues_

std::string protocols::hbnet::HBNet::des_residues_

private

Referenced by apply(), parse_my_tag(), and setup().

◆ extend_existing_networks_

bool protocols::hbnet::HBNet::extend_existing_networks_

private

Referenced by apply(), get_extend_existing_networks(), HBNet(), output_networks(), parse_my_tag(), set_extend_existing_networks(), set_only_extend_existing(), and setup().

◆ find_native_

bool protocols::hbnet::HBNet::find_native_

private

Referenced by find_native(), get_native_networks(), HBNet(), output_networks(), parse_my_tag(), set_find_native(), set_find_only_native(), and setup().

◆ hb_database_

core::scoring::hbonds::HBondDatabaseCOP protocols::hbnet::HBNet::hb_database_

private

Referenced by MC_traverse_IG().

◆ hbond_default_

std::string const protocols::hbnet::HBNet::hbond_default_

private

◆ hbond_disallow_

std::string protocols::hbnet::HBNet::hbond_disallow_

private

◆ hbond_disallow_default_

std::string const protocols::hbnet::HBNet::hbond_disallow_default_

private

◆ hbond_graph_

core::scoring::hbonds::graph::HBondGraphOP protocols::hbnet::HBNet::hbond_graph_

private

Referenced by add_residue_to_network_state(), get_next_node(), initialize_hbond_graph(), MC_branch_overlapping_networks(), MC_traverse_IG(), monte_carlo_net_clash(), monte_carlo_seed_is_dead_end(), network_state_is_done_growing(), register_clash(), and run().

◆ hydrogen_bond_threshold_

core::Real protocols::hbnet::HBNet::hydrogen_bond_threshold_

private

Referenced by apply(), check_clash(), get_native_networks(), parse_my_tag(), rec_trav_native(), run(), search_IG_for_networks(), and traverse_native().

◆ hydroxyls_must_donate_

bool protocols::hbnet::HBNet::hydroxyls_must_donate_

private

Referenced by find_unsats(), and parse_my_tag().

◆ ig_

core::pack::interaction_graph::InteractionGraphBaseOP protocols::hbnet::HBNet::ig_

private

Referenced by apply(), check_clash(), MC_traverse_IG(), net_clash(), recursive_traverse(), run(), search_IG_for_networks(), and traverse_IG().

◆ init_scorefxn_

core::scoring::ScoreFunctionOP protocols::hbnet::HBNet::init_scorefxn_

private

Referenced by net_clash(), and run().

◆ input_hbnet_info_residues_

core::select::residue_selector::ResidueSubset protocols::hbnet::HBNet::input_hbnet_info_residues_

private

Referenced by apply(), and setup().

◆ keep_existing_networks_

bool protocols::hbnet::HBNet::keep_existing_networks_

private

Referenced by apply(), get_keep_existing_networks(), output_networks(), parse_my_tag(), set_keep_existing_networks(), and setup().

◆ keep_start_selector_rotamers_fixed_

bool protocols::hbnet::HBNet::keep_start_selector_rotamers_fixed_

private

Referenced by parse_my_tag(), and setup().

◆ max_lig_unsat_

core::Size protocols::hbnet::HBNet::max_lig_unsat_

private

Referenced by select_best_networks().

◆ max_mc_nets_

core::Size protocols::hbnet::HBNet::max_mc_nets_

private

Referenced by append_to_network_vector(), parse_my_tag(), and set_monte_carlo_data_to_default().

◆ max_network_size_

core::Size protocols::hbnet::HBNet::max_network_size_

private

Referenced by get_max_networks_size(), parse_my_tag(), recursive_traverse(), select_best_networks(), and set_max_networks_size().

◆ max_rep_

core::Size protocols::hbnet::HBNet::max_rep_

private

Referenced by parse_my_tag(), and run().

◆ max_replicates_before_branch_

core::Size protocols::hbnet::HBNet::max_replicates_before_branch_

private

Referenced by parse_my_tag(), and run().

◆ max_replicates_before_unsat_check_

core::Size protocols::hbnet::HBNet::max_replicates_before_unsat_check_

private

Referenced by append_to_network_vector(), parse_my_tag(), and run().

◆ max_unsat_Hpol_

core::Size protocols::hbnet::HBNet::max_unsat_Hpol_

private

Referenced by get_max_unsat(), parse_my_tag(), select_best_networks(), and set_max_unsat().

◆ merged_vecs_

std::vector< std::vector< core::Size > > protocols::hbnet::HBNet::merged_vecs_

private

Referenced by branch_overlapping_networks(), and rec_set_intersection().

◆ min_boundary_res_

core::Size protocols::hbnet::HBNet::min_boundary_res_

private

Referenced by parse_my_tag(), and select_best_networks().

◆ min_core_res_

core::Size protocols::hbnet::HBNet::min_core_res_

private

Referenced by parse_my_tag(), and select_best_networks().

◆ min_network_size_

core::Size protocols::hbnet::HBNet::min_network_size_

private

Referenced by get_min_networks_size(), parse_my_tag(), select_best_networks(), and set_min_networks_size().

◆ min_percent_hbond_capacity_

core::Real protocols::hbnet::HBNet::min_percent_hbond_capacity_

private

Referenced by parse_my_tag(), and select_best_networks().

◆ min_unique_networks_

core::Size protocols::hbnet::HBNet::min_unique_networks_

private

Referenced by parse_my_tag(), and select_best_networks().

◆ minimize_

bool protocols::hbnet::HBNet::minimize_

private

Referenced by parse_my_tag(), and select_best_networks().

◆ monte_carlo_branch_

bool protocols::hbnet::HBNet::monte_carlo_branch_

private

Referenced by net_clash(), parse_my_tag(), run(), search_IG_for_networks(), set_monte_carlo_branch(), and set_monte_carlo_data_to_default().

◆ monte_carlo_seed_must_be_buried_

bool protocols::hbnet::HBNet::monte_carlo_seed_must_be_buried_

private

Referenced by edge_can_yield_monte_carlo_seed(), parse_my_tag(), set_monte_carlo_data_to_default(), and set_monte_carlo_seed_must_be_buried().

◆ monte_carlo_seed_must_be_fully_buried_

bool protocols::hbnet::HBNet::monte_carlo_seed_must_be_fully_buried_

private

Referenced by edge_can_yield_monte_carlo_seed(), parse_my_tag(), set_monte_carlo_data_to_default(), and set_monte_carlo_seed_must_be_fully_buried().

◆ monte_carlo_seed_threshold_

core::Real protocols::hbnet::HBNet::monte_carlo_seed_threshold_

private

Referenced by MC_traverse_IG(), parse_my_tag(), set_monte_carlo_data_to_default(), and set_monte_carlo_seed_threshold().

◆ monte_carlo_seeds_

utility::vector1< core::scoring::hbonds::graph::HBondEdge const * > protocols::hbnet::HBNet::monte_carlo_seeds_

private

Referenced by apply(), MC_branch_overlapping_networks(), MC_traverse_IG(), and set_monte_carlo_data_to_default().

◆ multi_component_

bool protocols::hbnet::HBNet::multi_component_

private

Referenced by get_ind_res(), multi_component(), and set_symmetry().

◆ native_networks_

std::vector< HBondNetStructOP > protocols::hbnet::HBNet::native_networks_

private

Referenced by apply(), get_native_networks(), get_native_vec(), output_networks(), and setup().

◆ network_vector_

std::vector< HBondNetStructOP > protocols::hbnet::HBNet::network_vector_

private

Referenced by apply(), branch_overlapping_networks(), get_native_networks(), get_net_vec(), get_network_by_id(), get_networks(), output_networks(), rec_set_intersection(), remove_replicate_networks(), run(), select_best_networks(), and store_network().

◆ no_heavy_unsats_allowed_

bool protocols::hbnet::HBNet::no_heavy_unsats_allowed_

private

Referenced by parse_my_tag(), and select_best_networks().

◆ onebody_hb_threshold_

core::Real protocols::hbnet::HBNet::onebody_hb_threshold_

private

Referenced by MC_traverse_IG(), parse_my_tag(), and traverse_IG().

◆ only_extend_existing_

bool protocols::hbnet::HBNet::only_extend_existing_

private

Referenced by get_only_extend_existing(), HBNet(), parse_my_tag(), set_only_extend_existing(), and setup().

◆ only_native_

bool protocols::hbnet::HBNet::only_native_

private

Referenced by apply(), branch_overlapping_networks(), get_native_networks(), HBNet(), only_native(), output_networks(), parse_my_tag(), remove_replicate_networks(), run(), set_find_only_native(), and setup().

◆ orig_pose_

core::pose::PoseOP protocols::hbnet::HBNet::orig_pose_

private

Referenced by apply(), chain_for_resid(), get_additional_output(), get_num_native_rot(), get_num_native_seq(), get_orig_pose(), MC_traverse_IG(), minimize_network(), nonconst_get_orig_pose(), output_networks(), place_rots_on_pose(), rec_trav_native(), recursive_traverse(), set_orig_pose(), traverse_IG(), and traverse_native().

◆ output_poly_ala_background_

bool protocols::hbnet::HBNet::output_poly_ala_background_

private

Referenced by apply(), get_additional_output(), output_networks(), and parse_my_tag().

◆ output_vector_

std::vector< std::set< core::Size > > protocols::hbnet::HBNet::output_vector_

private

Referenced by apply(), get_additional_output(), get_output_vector(), and output_networks().

◆ packer_neighbor_graph_

utility::graph::GraphOP protocols::hbnet::HBNet::packer_neighbor_graph_

private

Referenced by apply(), get_packer_graph(), MC_traverse_IG(), and run().

◆ rotamer_links_

core::pack::rotamer_set::RotamerLinksCOP protocols::hbnet::HBNet::rotamer_links_

private

Referenced by apply(), and setup().

◆ rotamer_sets_

core::pack::rotamer_set::RotamerSetsOP protocols::hbnet::HBNet::rotamer_sets_

private

Referenced by append_to_network_vector(), apply(), chain_for_moltenres(), check_clash(), edge_can_yield_monte_carlo_seed(), estimate_saturation(), get_aa_for_state(), initialize_hbond_graph(), MC_traverse_IG(), monte_carlo_net_clash(), net_clash(), network_already_stored(), place_rots_on_pose(), recursive_traverse(), run(), setup(), and traverse_IG().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::hbnet::HBNet::scorefxn_

private

Referenced by apply(), minimize_network(), and set_score_function().

◆ secondary_search_

bool protocols::hbnet::HBNet::secondary_search_

private

Referenced by parse_my_tag(), and recursive_traverse().

◆ secondary_threshold_

core::Real protocols::hbnet::HBNet::secondary_threshold_

private

Referenced by MC_traverse_IG(), parse_my_tag(), and recursive_traverse().

◆ show_task_

bool protocols::hbnet::HBNet::show_task_

private

Referenced by parse_my_tag(), and setup().

◆ start_res_vec_

std::set< core::Size > protocols::hbnet::HBNet::start_res_vec_

private

Referenced by add_start_res(), apply(), edge_can_yield_monte_carlo_seed(), get_start_res_vec(), recursive_traverse(), run(), set_start_res_vec(), set_start_resnums(), setup(), setup_packer_task_and_starting_residues(), traverse_IG(), and traverse_native().

◆ start_selector_

core::select::residue_selector::ResidueSelectorOP protocols::hbnet::HBNet::start_selector_

private

Referenced by apply(), and parse_my_tag().

◆ store_network_scores_in_pose_

bool protocols::hbnet::HBNet::store_network_scores_in_pose_

private

Referenced by parse_my_tag(), place_rots_on_pose(), and store_network_scores_in_pose().

◆ store_subnetworks_

bool protocols::hbnet::HBNet::store_subnetworks_

private

Referenced by apply(), branch_overlapping_networks(), parse_my_tag(), rec_set_intersection(), rec_trav_native(), and recursive_traverse().

◆ symm_info_

core::conformation::symmetry::SymmetryInfoCOP protocols::hbnet::HBNet::symm_info_

private

Referenced by check_clash(), get_ind_res(), get_symm_info(), MC_traverse_IG(), minimize_network(), net_clash(), recursive_traverse(), score_network_on_pose(), set_symm_info(), set_symmetry(), setup(), and traverse_IG().

◆ symmetric_

bool protocols::hbnet::HBNet::symmetric_

private

Referenced by add_residue_to_network_state(), check_clash(), get_ind_res(), MC_branch_overlapping_networks(), MC_traverse_IG(), minimize_network(), net_clash(), output_networks(), rec_trav_native(), recursive_traverse(), run(), score_network_on_pose(), set_symmetry(), setup(), symmetric(), traverse_IG(), traverse_native(), and water_clashes().

◆ task_

core::pack::task::PackerTaskOP protocols::hbnet::HBNet::task_

private

Referenced by append_to_network_vector(), get_task(), run(), set_task(), setup(), setup_packer_task_and_starting_residues(), and task_is_valid().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::hbnet::HBNet::task_factory_

private

Referenced by apply(), create_ptask(), setup_packer_task_and_starting_residues(), and task_factory().

◆ total_num_mc_runs_

core::Size protocols::hbnet::HBNet::total_num_mc_runs_

private

Referenced by MC_branch_overlapping_networks(), parse_my_tag(), set_monte_carlo_data_to_default(), and set_total_num_mc_runs().

◆ tyr_hydroxyls_must_donate_

bool protocols::hbnet::HBNet::tyr_hydroxyls_must_donate_

private

Referenced by find_unsats(), and parse_my_tag().

◆ upper_score_limit_

core::Real protocols::hbnet::HBNet::upper_score_limit_

private

Referenced by parse_my_tag(), and select_best_networks().

◆ upweight_twobody_

core::Real protocols::hbnet::HBNet::upweight_twobody_

private

Referenced by set_upweight_starting_twobody(), and upweight_starting_twobody_energy().

◆ use_pdb_numbering_

bool protocols::hbnet::HBNet::use_pdb_numbering_

private

Referenced by parse_my_tag(), and pdb_numbering().

◆ verbose_

bool protocols::hbnet::HBNet::verbose_

private

Referenced by apply(), branch_overlapping_networks(), find_unsats(), parse_my_tag(), remove_replicate_networks(), run(), select_best_networks(), and verbose().

◆ write_cst_files_

bool protocols::hbnet::HBNet::write_cst_files_

private

Referenced by apply(), get_additional_output(), output_networks(), and parse_my_tag().

◆ write_network_pdbs_

bool protocols::hbnet::HBNet::write_network_pdbs_

private

Referenced by output_networks(), and parse_my_tag().

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

src/protocols/hbnet/HBNet.hh
src/protocols/hbnet/HBNet.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ HBNet() [1/3]

◆ HBNet() [2/3]

◆ HBNet() [3/3]

◆ ~HBNet()

Member Function Documentation

◆ add_residue_to_network_state()

◆ add_start_res()

◆ append_to_network_vector()

◆ apply()

◆ atom_hbonds_to_bridging_water()

◆ attributes_for_hbnet()

◆ branch_overlapping_networks()

◆ chain_for_moltenres()

◆ chain_for_resid()

◆ check_clash()

◆ clone()

◆ create_ptask()

◆ edge_can_yield_monte_carlo_seed() [1/2]

◆ edge_can_yield_monte_carlo_seed() [2/2]

◆ estimate_saturation()

◆ find_native()

◆ find_unsats()

◆ fresh_instance()

◆ get_aa_for_state()

◆ get_additional_output()

◆ get_ala_pose()

◆ get_boundary_residues()

◆ get_boundary_selector()

◆ get_core_residues()

◆ get_core_selector()

◆ get_extend_existing_networks()

◆ get_file_name()

◆ get_ind_res()

◆ get_keep_existing_networks()

◆ get_max_networks_size()

◆ get_max_unsat()

◆ get_min_networks_size()

◆ get_name()

◆ get_native_networks()

◆ get_native_vec()

◆ get_net_vec()

◆ get_network_by_id()

◆ get_networks()

◆ get_next_node()

◆ get_num_native_rot()

◆ get_num_native_seq()

◆ get_only_extend_existing()

◆ get_orig_pose()

◆ get_output_vector()

◆ get_packer_graph()

◆ get_start_res_vec()

◆ get_symm_info()

◆ get_task()

◆ initialize_hbond_graph()

◆ is_sub_residues() [1/2]

◆ is_sub_residues() [2/2]

◆ ligand()

◆ MC_branch_overlapping_networks()

◆ MC_traverse_IG()

◆ merge_2_branched_networks() [1/2]

◆ merge_2_branched_networks() [2/2]

◆ minimize_network()

◆ monte_carlo_net_clash()

◆ monte_carlo_seed_is_dead_end()

◆ mover_name()

◆ multi_component() [1/2]

◆ multi_component() [2/2]

◆ net_clash() [1/2]

◆ net_clash() [2/2]

◆ network_already_stored()

◆ network_meets_final_criteria()

◆ network_meets_initial_criteria()

◆ network_state_is_done_growing()