#include <HBNetStapleInterface.hh>

Inheritance diagram for protocols::hbnet::HBNetStapleInterface:

[legend]

Public Member Functions
	HBNetStapleInterface ()

	HBNetStapleInterface (std::string const name)

	HBNetStapleInterface (core::scoring::ScoreFunctionCOP scorefxn, core::Size max_unsat_Hpol, core::Size min_network_size=3, core::Real hb_threshold=-0.5, 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)

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...

	~HBNetStapleInterface () override

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	setup_packer_task_and_starting_residues (core::pose::Pose const &pose) override

void	prepare_output () override

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

std::string	print_additional_headers () override

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

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

bool	state_is_starting_aa_type (core::Size const res, core::Size const rot_id) override

bool	pair_meets_starting_criteria (core::Size const res1, core::Size const rot1, core::Size const res2, core::Size const rot2) override

core::Real	scale_twobody_energy (core::Real input_twobody_energy, char res1, char res2) override

bool	same_helix (utility::vector1< std::pair< core::Size, core::Size > > const helix_boundaries, core::Size const r1, core::Size const r2)

bool	interhelical_contact (utility::vector1< std::pair< core::Size, core::Size > > const helix_boundaries, core::Size const r1, core::Size const r2, core::pose::Pose const &pose)

core::Size	get_helix_id (core::Size r1) const

void	rec_add_staple (std::vector< HBondNetStructOP >::const_iterator netit, std::set< core::Size > net_ids, core::Size staple_count)

bool	network_spans_all_helices (HBondNetStruct const &i) const

core::Size	num_helices_w_hbond (HBondNetStruct const &i) const

core::Size	num_helices_w_hbond (utility::vector1< HBondResStructCOP > const &residues) const

bool	has_pH_His (core::pose::Pose const &pose, HBondNetStruct &i)

bool	residues_are_interface_pairs (core::Size const res1, core::Size const res2)

core::Size	num_intermolecular_hbonds (HBondNetStruct &i, core::pose::Pose const &pose)

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

Public Member Functions inherited from protocols::hbnet::HBNet
	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

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

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

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

core::Real	upweight_starting_twobody_energy ()

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)

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

Static Public Member Functions inherited from protocols::hbnet::HBNet
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
bool	edge_can_yield_monte_carlo_seed (core::Size resid1, core::Size resid2) const override
	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...

Protected Member Functions inherited from protocols::hbnet::HBNet
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::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 Attributes
bool	all_helices_

bool	span_all_helices_

bool	only_symm_interfaces_

bool	allow_onebody_networks_

bool	his_tyr_

bool	pH_His_

bool	at_least_one_net_w_aromatic_sc_

bool	at_least_one_net_spans_all_helices_

bool	at_least_one_net_fully_satisfied_

bool	boundary_his_must_to_hbond_pos_charge_

bool	only_start_at_interface_pairs_

bool	use_aa_dependent_weights_

core::Size	min_networks_per_pose_

core::Size	max_networks_per_pose_

core::Size	combos_

core::Size	min_intermolecular_hbonds_

core::Size	min_helices_contacted_by_network_

core::Size	min_asp_glu_hbonds_

core::Real	interf_distance_

utility::vector1< core::Size >	jump_nums_

utility::vector1< std::pair< core::Size, core::Size > >	helix_boundaries_

utility::vector1< std::list< core::Size > >	pair_lists_vec_

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

◆ HBNetStapleInterface() [1/3]

protocols::hbnet::HBNetStapleInterface::HBNetStapleInterface ( )

◆ HBNetStapleInterface() [2/3]

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

◆ HBNetStapleInterface() [3/3]

protocols::hbnet::HBNetStapleInterface::HBNetStapleInterface	(	core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size	max_unsat_Hpol,
		core::Size	min_network_size = `3`,
		core::Real	hb_threshold = `-0.5`,
		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`
	)

◆ ~HBNetStapleInterface()

protocols::hbnet::HBNetStapleInterface::~HBNetStapleInterface ( )

overridedefault

Member Function Documentation

◆ clone()

moves::MoverOP protocols::hbnet::HBNetStapleInterface::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::hbnet::HBNet.

◆ edge_can_yield_monte_carlo_seed()

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

inlineoverrideprotectedvirtual

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 from protocols::hbnet::HBNet.

References all_helices_, protocols::hbnet::HBNet::chain_for_resid(), protocols::hbnet::HBNet::edge_can_yield_monte_carlo_seed(), and protocols::hbnet::HBNet::symmetric().

◆ fresh_instance()

moves::MoverOP protocols::hbnet::HBNetStapleInterface::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::hbnet::HBNet.

◆ get_helix_id()

Size protocols::hbnet::HBNetStapleInterface::get_helix_id ( core::Size r1 ) const

returns false if residues is not part of a helix

References helix_boundaries_, and protocols::hybridization::r1.

Referenced by num_helices_w_hbond().

◆ get_name()

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

overridevirtual

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

Reimplemented from protocols::hbnet::HBNet.

References mover_name().

◆ has_pH_His()

bool protocols::hbnet::HBNetStapleInterface::has_pH_His	(	core::pose::Pose const &	pose,
		HBondNetStruct &	i
	)

References core::pose::Pose::chain(), protocols::hbnet::HBNet::get_symm_info(), protocols::hbnet::HBondNetStruct::hbond_vec, protocols::hbnet::HBNet::multi_component(), core::conformation::Residue::name1(), protocols::hbnet::network_contains_aa(), core::pose::Pose::residue(), and protocols::hbnet::TR().

Referenced by network_meets_final_criteria().

◆ interhelical_contact()

bool protocols::hbnet::HBNetStapleInterface::interhelical_contact	(	utility::vector1< std::pair< core::Size, core::Size > > const	helix_boundaries,
		core::Size const	r1,
		core::Size const	r2,
		core::pose::Pose const &	pose
	)

returns false if either of the residues are not Helix (H); returns true if residues contact eachother from different helices (interhelical contact)

References interf_distance_, core::conformation::Residue::nbr_atom_xyz(), protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue(), and same_helix().

Referenced by setup_packer_task_and_starting_residues().

◆ mover_name()

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

static

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

◆ network_meets_final_criteria()

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

overridevirtual

final criteria that reuqires network rotamers placed on pose

Reimplemented from protocols::hbnet::HBNet.

◆ network_meets_initial_criteria()

bool protocols::hbnet::HBNetStapleInterface::network_meets_initial_criteria ( HBondNetStruct const & )

overridevirtual

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

Reimplemented from protocols::hbnet::HBNet.

References min_helices_contacted_by_network_, num_helices_w_hbond(), and protocols::hbnet::HBNet::symmetric().

◆ network_spans_all_helices()

bool protocols::hbnet::HBNetStapleInterface::network_spans_all_helices ( HBondNetStruct const & i ) const

References helix_boundaries_, and num_helices_w_hbond().

Referenced by prepare_output().

◆ num_helices_w_hbond() [1/2]

Size protocols::hbnet::HBNetStapleInterface::num_helices_w_hbond ( HBondNetStruct const & i ) const

References protocols::hbnet::HBondNetStruct::asymm_residues, and protocols::hbnet::HBondNetStruct::residues.

Referenced by network_meets_final_criteria(), network_meets_initial_criteria(), network_spans_all_helices(), and print_additional_info_for_net().

◆ num_helices_w_hbond() [2/2]

Size protocols::hbnet::HBNetStapleInterface::num_helices_w_hbond ( utility::vector1< HBondResStructCOP > const & residues ) const

References get_helix_id(), and helix_boundaries_.

◆ num_intermolecular_hbonds()

Size protocols::hbnet::HBNetStapleInterface::num_intermolecular_hbonds	(	HBondNetStruct &	i,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::chain(), protocols::hbnet::HBondNetStruct::hbond_vec, core::conformation::Residue::name1(), and core::pose::Pose::residue().

Referenced by network_meets_final_criteria(), and print_additional_info_for_net().

◆ pair_meets_starting_criteria()

bool protocols::hbnet::HBNetStapleInterface::pair_meets_starting_criteria	(	core::Size const	res1,
		core::Size const	rot1,
		core::Size const	res2,
		core::Size const	rot2
	)

overridevirtual

Reimplemented from protocols::hbnet::HBNet.

References protocols::hbnet::HBNet::get_aa_for_state(), his_tyr_, only_start_at_interface_pairs_, pH_His_, residues_are_interface_pairs(), protocols::jumping::rot1, and protocols::jumping::rot2.

◆ parse_my_tag()

void protocols::hbnet::HBNetStapleInterface::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::hbnet::HBNet.

References all_helices_, allow_onebody_networks_, at_least_one_net_fully_satisfied_, at_least_one_net_spans_all_helices_, at_least_one_net_w_aromatic_sc_, boundary_his_must_to_hbond_pos_charge_, combos_, his_tyr_, interf_distance_, jump_nums_, max_networks_per_pose_, min_asp_glu_hbonds_, min_helices_contacted_by_network_, min_intermolecular_hbonds_, min_networks_per_pose_, only_start_at_interface_pairs_, only_symm_interfaces_, protocols::hbnet::HBNet::parse_my_tag(), pH_His_, protocols::hbnet::HBNet::set_upweight_starting_twobody(), span_all_helices_, protocols::kinmatch::str(), and use_aa_dependent_weights_.

◆ prepare_output()

void protocols::hbnet::HBNetStapleInterface::prepare_output ( )

overridevirtual

◆ print_additional_headers()

std::string protocols::hbnet::HBNetStapleInterface::print_additional_headers ( )

overridevirtual

Reimplemented from protocols::hbnet::HBNet.

References min_helices_contacted_by_network_, and min_intermolecular_hbonds_.

◆ print_additional_info_for_net()

std::string protocols::hbnet::HBNetStapleInterface::print_additional_info_for_net	(	HBondNetStruct &	i,
		core::pose::Pose const &	pose
	)

overridevirtual

Reimplemented from protocols::hbnet::HBNet.

References min_helices_contacted_by_network_, min_intermolecular_hbonds_, num_helices_w_hbond(), and num_intermolecular_hbonds().

◆ provide_xml_schema()

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

static

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

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

◆ rec_add_staple()

void protocols::hbnet::HBNetStapleInterface::rec_add_staple	(	std::vector< HBondNetStructOP >::const_iterator	netit,
		std::set< core::Size >	net_ids,
		core::Size	staple_count
	)

References combos_, core::sequence::end, protocols::hbnet::HBNet::get_net_vec(), protocols::hbnet::HBNet::get_network_by_id(), protocols::hbnet::HBNet::get_output_vector(), protocols::hbnet::HBNet::is_sub_residues(), max_networks_per_pose_, min_networks_per_pose_, and protocols::hbnet::HBNet::net_clash().

Referenced by prepare_output().

◆ residues_are_interface_pairs()

bool protocols::hbnet::HBNetStapleInterface::residues_are_interface_pairs	(	core::Size const	res1,
		core::Size const	res2
	)

References core::sequence::end, protocols::hbnet::HBNet::get_ind_res(), protocols::hbnet::HBNet::get_orig_pose(), and pair_lists_vec_.

Referenced by pair_meets_starting_criteria().

◆ same_helix()

bool protocols::hbnet::HBNetStapleInterface::same_helix	(	utility::vector1< std::pair< core::Size, core::Size > > const	helix_boundaries,
		core::Size const	r1,
		core::Size const	r2
	)