#include <HotspotStubSet.hh>

Inheritance diagram for protocols::hotspot_hashing::HotspotStubSet:

Public Types
typedef std::multimap< core::Real, HotspotStubOP >	Hotspots

typedef std::map< std::string, Hotspots >	Hs_map

typedef std::pair< std::string, std::pair< core::Real, HotspotStubOP > >	Hs_data

typedef std::vector< Hs_data >	Hs_vec

typedef Hs_vec::iterator	iterator

typedef Hs_vec::const_iterator	const_iterator

Public Member Functions
	HotspotStubSet ()

	HotspotStubSet (HotspotStubSet const &init)

	HotspotStubSet (HotspotStubSet &&)=default
	Move constructor (mainly for copy/swap idiom) We're just moving the structure from one address to the other, so a default bitwise copy is appropriate. More...

HotspotStubSet &	operator= (HotspotStubSet &&)=default
	Move assigment operator (mainly for copy/swap idiom) More...

HotspotStubSet &	operator= (HotspotStubSet const &rhs)
	Assigment operator, needed as copy constructor is specified. More...

	~HotspotStubSet () override

void	clear ()

HotspotStubSet::const_iterator	begin () const

HotspotStubSet::const_iterator	end () const

HotspotStubSet::iterator	begin ()

HotspotStubSet::iterator	end ()

core::Size	hotspot_length () const
	set length of hotspot peptide used for finding stubs. Default=1, Hotspot stored in set will always be only 1 residue More...

void	hotspot_length (core::Size const length)

HotspotStubSetOP	colonyE ()
	returns a new stub_set with stub scores recalculated by colony energy (Xiang, Soto, and Honig PNAS 2002) More...

HotspotStubSetOP	cluster ()
	cluster stubs, returning a new stubset of cluster centers for each residue More...

Hotspots	retrieve (std::string const &residue_name3)
	retrieve all stubs with a given residue name More...

Hotspots::const_iterator	get_stub (std::string const &residue_name3, core::Real const score) const
	gets a stub from the stub_set_. A version returning an OP is private More...

HotspotStubSetOP	subset (std::string const &residue_name3, core::Real const scorecut)

HotspotStubSetOP	subset (core::Real const scorecut) const
	build a new stubset containing stubs that pass a score cutoff More...

HotspotStubCOP	get_best_energy_stub () const
	gets the best energy stub in the set More...

HotspotStubCOP	get_nearest_stub (core::conformation::ResidueCOP stub) const
	get the stub that's nearest to a residue More...

std::set< std::pair< std::string, core::Real > >	find_neighboring_stubs (HotspotStubCOP stub) const
	finds neighbors to stub based on distance between atoms. More...

void	remove_stubs_from_set (std::set< std::pair< std::string, core::Real > > const &)
	removes neighbors of stub based on repulsive energy between the pair of residues More...

void	remove_random_stubs_from_set (int const num_to_remove)

bool	remove_stub (HotspotStubCOP stub)
	removes a single stub. Reports false if stub is not found More...

void	read_data (std::string const &filename)
	add to stubset by reading from a file More...

void	fill (core::pose::Pose const &reference_pose, core::scoring::ScoreFunctionCOP scorefxn_in, std::string const &residue_name3, core::Size const n_stubs)
	fill the stub set with n_stubs by Rosetta residue name More...

void	fill (core::pose::Pose const &reference_pose, core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const target, core::Real const distance, std::string const &residue_name3, core::Size const n_stubs)
	only keep stubs within a certain distance of a residue on the target pose. More...

HotspotStubSetOP	rescore (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn)
	rescore all stubs in this set based on current flags (eg - sc_only() ) More...

void	autofill (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const n_stubs)
	fill the stub set with n_stubs each of A, R, N, D, E, Q, H, I, L, K, M, P, F, S, T, W, Y, and V More...

void	autofill (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const target, core::Real const distance, core::Size const n_stubs)

void	score_threshold (core::Real const threshold)
	only accept stubs that score better than this threshold (default is -1.0) More...

void	write_all (std::string const &filename) const
	write all stubs contained in this set to filename More...

void	write_stub (utility::io::ozstream &outstream, HotspotStubCOP stub, std::string const &tag) const
	write one stub with a user-supplied tag More...

void	pair_with_scaffold (core::pose::Pose const &pose, core::Size const partner, protocols::filters::FilterCOP filter)
	associate all stubs in the set with a scaffold partner More...

void	filter (protocols::filters::FilterCOP filter)
	set the filter to use for scaffold matching within this set More...

bool	sc_only () const
	true if these stubs are sidechain-only (defaults true) More...

void	sc_only (bool sc_switch)
	set whether or not sidechains are included More...

core::Size	size () const
	how many total stubs are in the set (all residues)? More...

core::Size	size (std::string const &resname)
	how many stubs are in the set by residue? More...

HotspotStubOP	random_stub ()
	returns a random stub either from the entire set or based on residue name More...

HotspotStubOP	random_stub (std::string const &resname)

void	add_hotspot_constraints_to_pose (core::pose::Pose &pose, core::Size const partner, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false)
	Sets up constraints using a given partner (auto choose packer task and fixed reference atom) More...

void	add_hotspot_constraints_to_wholepose (core::pose::Pose &pose, core::Size const partner, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false)
	utility function to add hotspot bbcst's to a pose More...

void	add_hotspot_constraints_to_pose (core::pose::Pose &pose, core::id::AtomID const &fixed_atom, core::pack::task::PackerTaskCOP const packer_task, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false)
	Sets up constraints with user-supplied packer task and fixed reference atom. More...

void	add_hotspot_constraints_to_wholepose (core::pose::Pose &pose, core::id::AtomID const &fixed_atom, core::pack::task::PackerTaskCOP const packer_task, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false)
	Sets up constraints with user-supplied packer task and fixed reference atom. More...

bool	remove_all_hotspot_constraints (core::pose::Pose &pose) const
	remove all ambiguous constraints that contain backbone_stub_constraints from the supplied pose More...

void	set_chain_to_design (core::Size const chain_to_design=2)

core::pack::task::PackerTaskOP	prepare_hashing_packer_task_ (core::pose::Pose const &pose, core::Size const chain_to_redesign=2)

core::scoring::constraints::ConstraintCOPs	constraints () const
	return bbcst's associatied with this stub set More...

void	add_stub_ (HotspotStubCOP stub)

void	add_stub_set (HotspotStubSet const &stubset)

Private Member Functions
void	handshake_stub_sets (void)
	clears stub_set_vec_ and inserts all the elements in stub_set_ to it. More...

void	create_hotspot_after_pose (core::pose::Pose &pose, std::string const &resname)

void	setup_hotspot_foldtree_ (core::pose::Pose &pose)
	set up foldtree for residue docking. If target_res is defined, takes that as connection point. Assumes hotspot to dock is last res in the pose! Assumes monomeric fold_tree! More...

core::Size	stub_offset ()
	utility function to find distance of stub from the end of the pose. More...

core::Real	get_residue_score_ (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const seqpos)
	utility function to calculate interaction energy for a single residue More...

core::Real	evaluate_stub_bumps_ (core::conformation::Residue const &placed_stub_residue, core::pose::Pose const &unbound_pose, core::Size const resnum, core::scoring::TenANeighborGraph const &unbound_neighbor_graph, core::scoring::ScoreFunctionCOP const &bump_scorefxn, core::Real const &max_bump_energy)

core::Real	evaluate_stub_self_energy_ (core::conformation::Residue const &stub_residue, core::pose::Pose const &unbound_pose, core::Size const resnum, core::scoring::TenANeighborGraph const &unbound_neighbor_graph, core::scoring::ScoreFunctionCOP const &full_scorefxn)

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

Friends
class	HotspotStub

Member Typedef Documentation

◆ const_iterator

typedef Hs_vec::const_iterator protocols::hotspot_hashing::HotspotStubSet::const_iterator

◆ Hotspots

typedef std::multimap< core::Real, HotspotStubOP > protocols::hotspot_hashing::HotspotStubSet::Hotspots

◆ Hs_data

typedef std::pair< std::string, std::pair< core::Real, HotspotStubOP > > protocols::hotspot_hashing::HotspotStubSet::Hs_data

◆ Hs_map

typedef std::map< std::string, Hotspots > protocols::hotspot_hashing::HotspotStubSet::Hs_map

◆ Hs_vec

typedef std::vector< Hs_data > protocols::hotspot_hashing::HotspotStubSet::Hs_vec

◆ iterator

typedef Hs_vec::iterator protocols::hotspot_hashing::HotspotStubSet::iterator

Constructor & Destructor Documentation

◆ HotspotStubSet() [1/3]

protocols::hotspot_hashing::HotspotStubSet::HotspotStubSet ( )

References set_chain_to_design().

◆ HotspotStubSet() [2/3]

protocols::hotspot_hashing::HotspotStubSet::HotspotStubSet ( HotspotStubSet const & init )

◆ HotspotStubSet() [3/3]

protocols::hotspot_hashing::HotspotStubSet::HotspotStubSet ( HotspotStubSet && )

default

Move constructor (mainly for copy/swap idiom) We're just moving the structure from one address to the other, so a default bitwise copy is appropriate.

◆ ~HotspotStubSet()

protocols::hotspot_hashing::HotspotStubSet::~HotspotStubSet ( )

overridedefault

Member Function Documentation

◆ add_hotspot_constraints_to_pose() [1/2]

void protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose	(	core::pose::Pose &	pose,
		core::id::AtomID const &	fixed_atom,
		core::pack::task::PackerTaskCOP const	packer_task,
		HotspotStubSetOP	hotspot_stub_set,
		core::Real const &	CB_force_constant,
		core::Real const &	worst_allowed_stub_bonus,
		bool const	apply_self_energies,
		core::Real const &	bump_cutoff,
		bool const	apply_ambiguous_constraints = `false`
	)

Sets up constraints with user-supplied packer task and fixed reference atom.

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, protocols::hotspot_hashing::accept, core::pose::Pose::add_constraints(), core::pose::Pose::chain(), constraints_, core::pack::task::TaskFactory::create_packer_task(), core::pose::Pose::energies(), core::scoring::envsmooth, evaluate_stub_bumps_(), evaluate_stub_self_energy_(), core::scoring::fa_dun, core::scoring::fa_rep, generate_unbound_pose_(), core::scoring::get_score_function_legacy(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::conformation::Residue::mainchain_torsions(), core::chemical::num_canonical_aas, core::conformation::Residue::orient_onto_residue(), core::pack::pack_rotamers(), core::pack::task::parse_resfile(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::hotspot_hashing::reject, core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::Energies::tenA_neighbor_graph(), protocols::hotspot_hashing::TR(), and core::scoring::hbonds::HBondOptions::use_hb_env_dep().

◆ add_hotspot_constraints_to_pose() [2/2]

void protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose	(	core::pose::Pose &	pose,
		core::Size const	partner,
		HotspotStubSetOP	hotspot_stub_set,
		core::Real const &	CB_force_constant,
		core::Real const &	worst_allowed_stub_bonus,
		bool const	apply_self_energies,
		core::Real const &	bump_cutoff,
		bool const	apply_ambiguous_constraints = `false`
	)

Sets up constraints using a given partner (auto choose packer task and fixed reference atom)

utility function to add hotspot bbcst's to a pose

References core::conformation::Residue::atom_index(), prepare_hashing_packer_task_(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ add_hotspot_constraints_to_wholepose() [1/2]

void protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose	(	core::pose::Pose &	pose,
		core::id::AtomID const &	fixed_atom,
		core::pack::task::PackerTaskCOP const	packer_task,
		HotspotStubSetOP	hotspot_stub_set,
		core::Real const &	CB_force_constant,
		core::Real const &	worst_allowed_stub_bonus,
		bool const	apply_self_energies,
		core::Real const &	bump_cutoff,
		bool const	apply_ambiguous_constraints = `false`
	)

Sets up constraints with user-supplied packer task and fixed reference atom.

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, protocols::hotspot_hashing::accept, core::pose::Pose::add_constraints(), core::pose::Pose::chain(), constraints_, core::pack::task::TaskFactory::create_packer_task(), core::pose::Pose::energies(), core::scoring::envsmooth, evaluate_stub_bumps_(), evaluate_stub_self_energy_(), core::scoring::fa_dun, core::scoring::fa_rep, generate_unbound_pose_(), core::scoring::get_score_function_legacy(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::conformation::Residue::mainchain_torsions(), core::chemical::num_canonical_aas, core::conformation::Residue::orient_onto_residue(), core::pack::pack_rotamers(), core::pack::task::parse_resfile(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::hotspot_hashing::reject, core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::Energies::tenA_neighbor_graph(), protocols::hotspot_hashing::TR(), and core::scoring::hbonds::HBondOptions::use_hb_env_dep().

◆ add_hotspot_constraints_to_wholepose() [2/2]

void protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose	(	core::pose::Pose &	pose,
		core::Size const	partner,
		HotspotStubSetOP	hotspot_stub_set,
		core::Real const &	CB_force_constant,
		core::Real const &	worst_allowed_stub_bonus,
		bool const	apply_self_energies,
		core::Real const &	bump_cutoff,
		bool const	apply_ambiguous_constraints = `false`
	)

utility function to add hotspot bbcst's to a pose

References core::conformation::Residue::atom_index(), prepare_hashing_packer_task_(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ add_stub_()

void protocols::hotspot_hashing::HotspotStubSet::add_stub_ ( HotspotStubCOP stub )

References handshake_stub_sets(), and stub_set_.

Referenced by add_stub_set(), fill(), and read_data().

◆ add_stub_set()

void protocols::hotspot_hashing::HotspotStubSet::add_stub_set ( HotspotStubSet const & stubset )

References add_stub_().

◆ autofill() [1/2]

void protocols::hotspot_hashing::HotspotStubSet::autofill	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	n_stubs
	)

fill the stub set with n_stubs each of A, R, N, D, E, Q, H, I, L, K, M, P, F, S, T, W, Y, and V

References fill().

Referenced by autofill().

◆ autofill() [2/2]

void protocols::hotspot_hashing::HotspotStubSet::autofill	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	target,
		core::Real const	distance,
		core::Size const	n_stubs
	)

References autofill(), core::kinematics::distance(), core::pose::Pose::size(), target_distance_, and target_resnum_.

◆ begin() [1/2]

HotspotStubSet::iterator protocols::hotspot_hashing::HotspotStubSet::begin ( )

inline

References size(), and stub_set_vec_.

◆ begin() [2/2]

HotspotStubSet::const_iterator protocols::hotspot_hashing::HotspotStubSet::begin ( ) const

inline

References size(), and stub_set_vec_.

◆ clear()

void protocols::hotspot_hashing::HotspotStubSet::clear ( )

References handshake_stub_sets(), and stub_set_.

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply().

◆ cluster()

HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::cluster ( )

cluster stubs, returning a new stubset of cluster centers for each residue

clusters all residues within this stubset on a per-restype basis and returns a new clustered stubset

References protocols::cluster::APCluster::cluster(), protocols::cluster::APCluster::get_all_exemplars(), protocols::cluster::APCluster::get_cluster_for(), protocols::antibody::lambda, protocols::hotspot_hashing::residue_sc_rmsd_no_super(), retrieve(), core::scoring::rms, protocols::hybridization::score, protocols::cluster::APCluster::set_sim(), and protocols::hotspot_hashing::TR().

◆ colonyE()

HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::colonyE ( )

returns a new stub_set with stub scores recalculated by colony energy (Xiang, Soto, and Honig PNAS 2002)

E = -ln (sum exp( -E(j) - rmsd(ij)^3/6L ) )

References chain_to_design_, filter_, pose_, protocols::hotspot_hashing::residue_sc_rmsd_no_super(), retrieve(), core::scoring::rms, and protocols::hotspot_hashing::TR().

◆ constraints()

core::scoring::constraints::ConstraintCOPs protocols::hotspot_hashing::HotspotStubSet::constraints ( ) const

return bbcst's associatied with this stub set

References constraints_.

◆ create_hotspot_after_pose()

void protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose	(	core::pose::Pose &	pose,
		std::string const &	resname
	)

private

Referenced by fill().

◆ end() [1/2]

HotspotStubSet::iterator protocols::hotspot_hashing::HotspotStubSet::end ( )

inline

References stub_set_vec_.

◆ end() [2/2]

HotspotStubSet::const_iterator protocols::hotspot_hashing::HotspotStubSet::end ( ) const

inline

References stub_set_vec_.

Referenced by protocols::hotspot_hashing::remove_hotspot_constraints_from_pose().

◆ evaluate_stub_bumps_()

core::Real protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_bumps_	(	core::conformation::Residue const &	placed_stub_residue,
		core::pose::Pose const &	unbound_pose,
		core::Size const	resnum,
		core::scoring::TenANeighborGraph const &	unbound_neighbor_graph,
		core::scoring::ScoreFunctionCOP const &	bump_scorefxn,
		core::Real const &	max_bump_energy
	)

private

References core::scoring::EMapVector::clear(), core::scoring::fa_rep, and core::pose::Pose::residue().

Referenced by add_hotspot_constraints_to_pose(), and add_hotspot_constraints_to_wholepose().

◆ evaluate_stub_self_energy_()

core::Real protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_self_energy_	(	core::conformation::Residue const &	stub_residue,
		core::pose::Pose const &	unbound_pose,
		core::Size const	resnum,
		core::scoring::TenANeighborGraph const &	unbound_neighbor_graph,
		core::scoring::ScoreFunctionCOP const &	full_scorefxn
	)

private

References core::scoring::EMapVector::clear(), core::scoring::EMapVector::dot(), core::pose::Pose::residue(), and protocols::hotspot_hashing::TR().

Referenced by add_hotspot_constraints_to_pose(), and add_hotspot_constraints_to_wholepose().

◆ fill() [1/2]

void protocols::hotspot_hashing::HotspotStubSet::fill	(	core::pose::Pose const &	reference_pose,
		core::scoring::ScoreFunctionCOP	scorefxn_in,
		core::Size const	target,
		core::Real const	distance,
		std::string const &	residue_name3,
		core::Size const	n_stubs
	)

only keep stubs within a certain distance of a residue on the target pose.

References core::kinematics::distance(), fill(), core::pose::Pose::size(), target_distance_, and target_resnum_.

◆ fill() [2/2]

void protocols::hotspot_hashing::HotspotStubSet::fill	(	core::pose::Pose const &	reference_pose,
		core::scoring::ScoreFunctionCOP	scorefxn_in,
		std::string const &	residue_name3,
		core::Size const	n_stubs
	)

fill the stub set with n_stubs by Rosetta residue name

References add_stub_(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), chain_to_design_, create_hotspot_after_pose(), core::scoring::ScoreFunctionFactory::create_score_function(), core::kinematics::distance(), filter_, core::pose::Pose::fold_tree(), get_residue_score_(), core::conformation::Residue::get_self_ptr(), core::pose::Pose::num_jump(), protocols::rigid::partner_downstream, protocols::rigid::partner_upstream, core::pose::Pose::residue(), protocols::hybridization::score, score_threshold_, setup_hotspot_foldtree_(), core::pose::Pose::size(), stub_offset(), protocols::hotspot_hashing::stub_tgt_angle(), target_distance_, target_resnum_, and protocols::hotspot_hashing::TR().

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply(), autofill(), and fill().

◆ filter()

void protocols::hotspot_hashing::HotspotStubSet::filter ( protocols::filters::FilterCOP filter )

set the filter to use for scaffold matching within this set

References filter_.

Referenced by pair_with_scaffold().

◆ find_neighboring_stubs()

std::set< std::pair< std::string, core::Real > > protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs ( HotspotStubCOP stub ) const

finds neighbors to stub based on distance between atoms.

References core::conformation::Residue::atom_begin(), core::conformation::Residue::atom_end(), and stub_set_.

◆ generate_unbound_pose_()

void protocols::hotspot_hashing::HotspotStubSet::generate_unbound_pose_ ( core::pose::Pose & pose )

private

References protocols::rigid::RigidBodyTransMover::apply(), protocols::rigid::RigidBodyTransMover::step_size(), and protocols::rigid::RigidBodyTransMover::trans_axis().

Referenced by add_hotspot_constraints_to_pose(), add_hotspot_constraints_to_wholepose(), and prepare_hashing_packer_task_().

◆ get_best_energy_stub()

HotspotStubCOP protocols::hotspot_hashing::HotspotStubSet::get_best_energy_stub ( ) const

gets the best energy stub in the set

References stub_set_.

◆ get_nearest_stub()

HotspotStubCOP protocols::hotspot_hashing::HotspotStubSet::get_nearest_stub ( core::conformation::ResidueCOP residue ) const

get the stub that's nearest to a residue

find stub nearest to residue based on CA-CA distance

References core::kinematics::distance(), and stub_set_.

◆ get_residue_score_()

core::Real protocols::hotspot_hashing::HotspotStubSet::get_residue_score_	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	seqpos
	)

private

utility function to calculate interaction energy for a single residue

References core::pose::Pose::append_residue_by_jump(), protocols::simple_ddg::DdgFilter::compute(), core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_range_slow(), hotspot_length(), core::pose::Pose::residue(), protocols::hybridization::score, and core::pose::Pose::size().

Referenced by fill(), and rescore().

◆ get_stub()

HotspotStubSet::Hotspots::const_iterator protocols::hotspot_hashing::HotspotStubSet::get_stub	(	std::string const &	residue_name3,
		core::Real const	score
	)		const

gets a stub from the stub_set_. A version returning an OP is private

References protocols::hybridization::score, and stub_set_.

Referenced by remove_stubs_from_set().

◆ handshake_stub_sets()

void protocols::hotspot_hashing::HotspotStubSet::handshake_stub_sets ( void )

private

clears stub_set_vec_ and inserts all the elements in stub_set_ to it.

remove all stubs from stub_set_vec_ and repopulate it with stub_set_

References stub_set_, and stub_set_vec_.

Referenced by add_stub_(), clear(), remove_stub(), and remove_stubs_from_set().

◆ hotspot_length() [1/2]

core::Size protocols::hotspot_hashing::HotspotStubSet::hotspot_length ( ) const

set length of hotspot peptide used for finding stubs. Default=1, Hotspot stored in set will always be only 1 residue

References hotspot_length_.

Referenced by create_hotspot_after_pose(), get_residue_score_(), setup_hotspot_foldtree_(), and stub_offset().

◆ hotspot_length() [2/2]

void protocols::hotspot_hashing::HotspotStubSet::hotspot_length ( core::Size const length )

References hotspot_length_.

◆ operator=() [1/2]

HotspotStubSet& protocols::hotspot_hashing::HotspotStubSet::operator= ( HotspotStubSet && )

default

Move assigment operator (mainly for copy/swap idiom)

◆ operator=() [2/2]

HotspotStubSet& protocols::hotspot_hashing::HotspotStubSet::operator= ( HotspotStubSet const & rhs )

inline

Assigment operator, needed as copy constructor is specified.

References core::id::swap().

◆ pair_with_scaffold()

void protocols::hotspot_hashing::HotspotStubSet::pair_with_scaffold	(	core::pose::Pose const &	pose,
		core::Size const	partner,
		protocols::filters::FilterCOP	filter
	)

associate all stubs in the set with a scaffold partner

set up scaffold_status_ for each stub included in this set

References chain_to_design_, filter(), filter_, pose_, stub_set_, protocols::hotspot_hashing::TR(), and protocols::hotspot_hashing::unchecked.

◆ prepare_hashing_packer_task_()

core::pack::task::PackerTaskOP protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_	(	core::pose::Pose const &	pose,
		core::Size const	chain_to_redesign = `2`
	)

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::aa_pro, core::scoring::calc_per_atom_sasa(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), generate_unbound_pose_(), core::pack::task::parse_resfile(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by add_hotspot_constraints_to_pose(), and add_hotspot_constraints_to_wholepose().

◆ random_stub() [1/2]

HotspotStubOP protocols::hotspot_hashing::HotspotStubSet::random_stub ( )

returns a random stub either from the entire set or based on residue name

References HotspotStub, core::scoring::rg, size(), and stub_set_.

◆ random_stub() [2/2]

HotspotStubOP protocols::hotspot_hashing::HotspotStubSet::random_stub ( std::string const & resname )

References HotspotStub, retrieve(), and core::scoring::rg.

◆ read_data()

void protocols::hotspot_hashing::HotspotStubSet::read_data ( std::string const & filename )

add to stubset by reading from a file

References add_stub_(), chain_to_design_, core::chemical::FA_STANDARD, protocols::abinitio::filename(), filter_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::hybridization::score, core::io::StructFileRepOptions::set_preserve_header(), size(), and protocols::hotspot_hashing::TR().

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply().

◆ remove_all_hotspot_constraints()

bool protocols::hotspot_hashing::HotspotStubSet::remove_all_hotspot_constraints ( core::pose::Pose & pose ) const

remove all ambiguous constraints that contain backbone_stub_constraints from the supplied pose

References constraints_, and core::pose::Pose::remove_constraints().

◆ remove_random_stubs_from_set()

void protocols::hotspot_hashing::HotspotStubSet::remove_random_stubs_from_set ( int const num_to_remove )

References remove_stub(), core::scoring::rg, size(), stub_set_vec_, and protocols::hotspot_hashing::TR().

◆ remove_stub()

bool protocols::hotspot_hashing::HotspotStubSet::remove_stub ( HotspotStubCOP stub )

removes a single stub. Reports false if stub is not found

removes the first occurence of stub in the stubset

References handshake_stub_sets(), stub_set_, and protocols::hotspot_hashing::TR().

Referenced by remove_random_stubs_from_set().

◆ remove_stubs_from_set()

void protocols::hotspot_hashing::HotspotStubSet::remove_stubs_from_set ( std::set< std::pair< std::string, core::Real > > const & stubs )

removes neighbors of stub based on repulsive energy between the pair of residues

removes a set of stubs from the stub_set_

References get_stub(), handshake_stub_sets(), and stub_set_.

◆ rescore()

HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::rescore	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

rescore all stubs in this set based on current flags (eg - sc_only() )

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_jump(), chain_to_design_, filter_, get_residue_score_(), core::pose::Pose::residue(), sc_only_, protocols::hybridization::score, core::chemical::SHOVE_BB, core::pose::Pose::size(), stub_set_, and protocols::hotspot_hashing::TR().

◆ retrieve()

HotspotStubSet::Hotspots protocols::hotspot_hashing::HotspotStubSet::retrieve ( std::string const & residue_name3 )

retrieve all stubs with a given residue name

References stub_set_, and protocols::hotspot_hashing::TR().

Referenced by cluster(), colonyE(), random_stub(), size(), and subset().

◆ sc_only() [1/2]

bool protocols::hotspot_hashing::HotspotStubSet::sc_only ( ) const

true if these stubs are sidechain-only (defaults true)

References sc_only_.

◆ sc_only() [2/2]

void protocols::hotspot_hashing::HotspotStubSet::sc_only ( bool sc_switch )

set whether or not sidechains are included

References sc_only_.

◆ score_threshold()

void protocols::hotspot_hashing::HotspotStubSet::score_threshold ( core::Real const threshold )

only accept stubs that score better than this threshold (default is -1.0)

References score_threshold_.

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply().

◆ set_chain_to_design()

void protocols::hotspot_hashing::HotspotStubSet::set_chain_to_design ( core::Size const chain_to_design = 2 )

References chain_to_design_.

Referenced by HotspotStubSet().

◆ setup_hotspot_foldtree_()

void protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_ ( core::pose::Pose & pose )

private

set up foldtree for residue docking. If target_res is defined, takes that as connection point. Assumes hotspot to dock is last res in the pose! Assumes monomeric fold_tree!

References core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::fold_tree(), hotspot_length(), core::pose::Pose::num_jump(), core::kinematics::FoldTree::reorder(), core::pose::residue_center_of_mass(), core::pose::Pose::size(), core::kinematics::FoldTree::slide_jump(), stub_offset(), target_distance_, target_resnum_, and protocols::hotspot_hashing::TR().

Referenced by fill().

◆ size() [1/2]

core::Size protocols::hotspot_hashing::HotspotStubSet::size ( ) const

how many total stubs are in the set (all residues)?

References stub_set_.

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply(), begin(), random_stub(), read_data(), remove_random_stubs_from_set(), and size().

◆ size() [2/2]

core::Size protocols::hotspot_hashing::HotspotStubSet::size ( std::string const & resname )

how many stubs are in the set by residue?

References retrieve(), and size().

◆ stub_offset()

core::Size protocols::hotspot_hashing::HotspotStubSet::stub_offset ( )

private

utility function to find distance of stub from the end of the pose.

utility function to find distance of a hotspot from the end of the current pose. Should be in middle or more C-terminal if hotspot_length is even

References hotspot_length().

Referenced by fill(), and setup_hotspot_foldtree_().

◆ subset() [1/2]

HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::subset ( core::Real const scorecut ) const

build a new stubset containing stubs that pass a score cutoff

References sc_only_, stub_set_, and protocols::hotspot_hashing::TR().

◆ subset() [2/2]

HotspotStubSetOP protocols::hotspot_hashing::HotspotStubSet::subset	(	std::string const &	residue_name3,
		core::Real const	scorecut
	)

References retrieve(), sc_only_, and protocols::hotspot_hashing::TR().

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply().

◆ write_all()

void protocols::hotspot_hashing::HotspotStubSet::write_all ( std::string const & filename ) const

write all stubs contained in this set to filename

References protocols::abinitio::filename(), stub_set_, protocols::hotspot_hashing::TR(), and write_stub().

Referenced by protocols::protein_interface_design::movers::HotspotHasherMover::apply().

◆ write_stub()

void protocols::hotspot_hashing::HotspotStubSet::write_stub	(	utility::io::ozstream &	outstream,
		HotspotStubCOP	stub,
		std::string const &	tag
	)		const

write one stub with a user-supplied tag

References core::io::pdb::dump_pdb_residue().

Referenced by write_all().

Friends And Related Function Documentation

◆ HotspotStub

friend class HotspotStub

friend

Referenced by random_stub().

Member Data Documentation

◆ chain_to_design_

core::Size protocols::hotspot_hashing::HotspotStubSet::chain_to_design_

private

Referenced by colonyE(), fill(), pair_with_scaffold(), read_data(), rescore(), and set_chain_to_design().

◆ constraints_

core::scoring::constraints::ConstraintCOPs protocols::hotspot_hashing::HotspotStubSet::constraints_

private

Referenced by add_hotspot_constraints_to_pose(), add_hotspot_constraints_to_wholepose(), constraints(), and remove_all_hotspot_constraints().

◆ filter_

protocols::filters::FilterCOP protocols::hotspot_hashing::HotspotStubSet::filter_

private

Referenced by colonyE(), fill(), filter(), pair_with_scaffold(), read_data(), and rescore().

◆ hotspot_length_

core::Size protocols::hotspot_hashing::HotspotStubSet::hotspot_length_

private

Referenced by hotspot_length().

◆ pose_

core::pose::PoseCOP protocols::hotspot_hashing::HotspotStubSet::pose_

private

Referenced by colonyE(), and pair_with_scaffold().

◆ sc_only_

bool protocols::hotspot_hashing::HotspotStubSet::sc_only_

private

Referenced by create_hotspot_after_pose(), rescore(), sc_only(), and subset().

◆ score_threshold_

core::Real protocols::hotspot_hashing::HotspotStubSet::score_threshold_

private

Referenced by fill(), and score_threshold().

◆ stub_set_

Hs_map protocols::hotspot_hashing::HotspotStubSet::stub_set_

private

Referenced by add_stub_(), clear(), find_neighboring_stubs(), get_best_energy_stub(), get_nearest_stub(), get_stub(), handshake_stub_sets(), pair_with_scaffold(), random_stub(), remove_stub(), remove_stubs_from_set(), rescore(), retrieve(), size(), subset(), and write_all().

◆ stub_set_vec_

Hs_vec protocols::hotspot_hashing::HotspotStubSet::stub_set_vec_

private

Referenced by begin(), end(), handshake_stub_sets(), and remove_random_stubs_from_set().

◆ target_distance_

core::Real protocols::hotspot_hashing::HotspotStubSet::target_distance_

private

Referenced by autofill(), create_hotspot_after_pose(), fill(), and setup_hotspot_foldtree_().

◆ target_resnum_

core::Size protocols::hotspot_hashing::HotspotStubSet::target_resnum_

private

Referenced by autofill(), create_hotspot_after_pose(), fill(), and setup_hotspot_foldtree_().

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

src/protocols/hotspot_hashing/HotspotStubSet.hh
src/protocols/hotspot_hashing/HotspotStubSet.cc

Private Attributes
Hs_map	stub_set_

Hs_vec	stub_set_vec_

bool	sc_only_

core::Size	target_resnum_

core::Real	target_distance_

core::Size	chain_to_design_

core::pose::PoseCOP	pose_

core::Real	score_threshold_

protocols::filters::FilterCOP	filter_

core::Size	hotspot_length_

core::scoring::constraints::ConstraintCOPs	constraints_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Member Typedef Documentation

◆ const_iterator

◆ Hotspots

◆ Hs_data

◆ Hs_map

◆ Hs_vec

◆ iterator

Constructor & Destructor Documentation

◆ HotspotStubSet() [1/3]

◆ HotspotStubSet() [2/3]

◆ HotspotStubSet() [3/3]

◆ ~HotspotStubSet()

Member Function Documentation

◆ add_hotspot_constraints_to_pose() [1/2]

◆ add_hotspot_constraints_to_pose() [2/2]

◆ add_hotspot_constraints_to_wholepose() [1/2]

◆ add_hotspot_constraints_to_wholepose() [2/2]

◆ add_stub_()

◆ add_stub_set()

◆ autofill() [1/2]

◆ autofill() [2/2]

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear()

◆ cluster()

◆ colonyE()

◆ constraints()

◆ create_hotspot_after_pose()

◆ end() [1/2]

◆ end() [2/2]

◆ evaluate_stub_bumps_()

◆ evaluate_stub_self_energy_()

◆ fill() [1/2]

◆ fill() [2/2]

◆ filter()

◆ find_neighboring_stubs()

◆ generate_unbound_pose_()

◆ get_best_energy_stub()

◆ get_nearest_stub()

◆ get_residue_score_()

◆ get_stub()

◆ handshake_stub_sets()

◆ hotspot_length() [1/2]

◆ hotspot_length() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ pair_with_scaffold()

◆ prepare_hashing_packer_task_()

◆ random_stub() [1/2]

◆ random_stub() [2/2]

◆ read_data()

◆ remove_all_hotspot_constraints()

◆ remove_random_stubs_from_set()

◆ remove_stub()

◆ remove_stubs_from_set()

◆ rescore()

◆ retrieve()

◆ sc_only() [1/2]

◆ sc_only() [2/2]

◆ score_threshold()

◆ set_chain_to_design()

◆ setup_hotspot_foldtree_()

◆ size() [1/2]

◆ size() [2/2]

◆ stub_offset()

◆ subset() [1/2]

◆ subset() [2/2]

◆ write_all()

◆ write_stub()

Friends And Related Function Documentation

◆ HotspotStub

Member Data Documentation

◆ chain_to_design_

◆ constraints_

◆ filter_