choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria. More...

#include <PlaceSimultaneouslyMover.hh>

Public Types
typedef std::pair < protocols::hotspot_hashing::HotspotStubSetOP, std::pair < protocols::hotspot_hashing::HotspotStubOP, core::Size > >	StubSetStubPos

typedef std::pair < protocols::simple_moves::DesignRepackMoverOP, core::Real >	MoverRealPair

typedef std::pair < simple_moves::DesignRepackMoverOP, bool >	DesignMoverFoldTreePair

typedef std::pair < simple_moves::DesignRepackMoverOP, core::Real >	DesignMoverRealPair

typedef std::pair < protocols::hotspot_hashing::HotspotStubSetOP, protocols::hotspot_hashing::HotspotStubOP >	StubsetStubPair
	ResidueAuction is keyed by energy => we select the residue,stub,stubset combination with the best energy for each stubset,stub combination. More...

typedef std::pair< core::Real, std::pair< core::Size, StubsetStubPair > >	ResidueAuctionItem

typedef std::multimap < core::Real, std::pair < core::Size, StubsetStubPair > >	ResidueAuction

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

Public Member Functions
	PlaceSimultaneouslyMover ()

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

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

virtual void	apply (core::pose::Pose &pose)
	a dummy apply so that instantiation of this baseclass would be possible. More...

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

bool	minimize_no_bb (core::pose::Pose &pose) const
	minimize towards clouds of stubs made up of all the stub sets More...

void	minimize_all (core::pose::Pose &pose, core::Size const minimization_steps) const
	minimize simultaneously towards the placed stubs from each of the stub sets returns false if one of the filters fails More...

bool	pair_sets_with_positions (core::pose::Pose &pose)
	pair each stub set with a position on the scaffold More...

void	design (core::pose::Pose &pose)
	conducts user-specified design movers. Returns true if the energy per residue filter passes for each of the placed hotspots More...

bool	place_stubs (core::pose::Pose &pose) const
	will be removed More...

virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

void	refresh_coordinate_constraints (core::pose::Pose &pose, core::Real const coord_sdev)
	removes and reinstates coordinate constraints for all placed hotspots according to coord_sdev More...

core::pack::task::PackerTaskOP	create_task_for_hotspot_packing (core::pose::Pose const &)

core::pack::task::PackerTaskOP	create_task_for_allhotspot_packing (core::pose::Pose const &)

void	add_coordinatecst_for_hotspot_packing (core::pose::Pose &)
	coordinate constraints to pose More...

void	stub_sets (utility::vector1< StubSetStubPos > const sets)

void	host_chain (core::Size const host_chain)

virtual	~PlaceSimultaneouslyMover ()

Public Member Functions inherited from protocols::simple_moves::DesignRepackMover
	DesignRepackMover ()

	DesignRepackMover (std::string const name)

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

void	min_rb (utility::vector1< bool > const min_rb)

void	min_rb (bool const min_rb)
	in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More...

utility::vector1< bool > const &	min_rb () const

bool	min_rb_set () const

void	min_sc (utility::vector1< bool > const &min_sc)

utility::vector1< bool > const &	min_sc () const

bool	min_sc_set () const

void	min_bb (utility::vector1< bool > const &min_bb)

utility::vector1< bool > const &	min_bb () const

bool	min_bb_set () const

bool	optimize_foldtree () const

void	optimize_foldtree (bool const opt)

void	prevent_repacking (utility::vector1< core::Size > const p)

utility::vector1< core::Size > const &	prevent_repacking () const

void	restrict_to_repacking (utility::vector1< core::Size > const p)

utility::vector1< core::Size > const &	restrict_to_repacking () const

void	design (bool const des)

bool	design () const

void	set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)

void	set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)

core::scoring::ScoreFunctionOP	scorefxn_repack () const

core::scoring::ScoreFunctionOP	scorefxn_minimize () const

core::pack::task::PackerTaskCOP	task () const

core::pack::task::PackerTaskOP &	task ()

void	clear_task ()
	after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More...

void	clear_task_factory ()

void	use_preset_task (bool const bt)

bool	use_preset_task () const

void	task_factory (core::pack::task::TaskFactoryOP p)

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

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

virtual	~DesignRepackMover ()

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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

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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

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...

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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Attributes
core::Size	host_chain_
	where is the stub to be placed More...

core::pose::Pose	saved_pose_

utility::vector1< StubSetStubPos >	stub_sets_
	stub sets and placed positions More...

utility::vector1< StubSetStubPos >	saved_stub_sets_

std::map < protocols::hotspot_hashing::HotspotStubSetOP, protocols::filters::FilterOP >	stub_set_filters_

core::Real	max_cb_cb_dist_
	the maximum distance for a stub to be considered a a neighbour to a host residue More...

core::Real	coor_cst_cutoff_

core::Real	stub_energy_threshold_
	Maximum per-residue energy the placed stub can have to be saved. More...

utility::vector1< MoverRealPair >	minimization_movers_

core::Size	minimization_repeats_before_placement_

core::Size	minimization_repeats_after_placement_

core::scoring::constraints::ConstraintCOPs	saved_bb_constraints_

protocols::filters::FilterOP	after_placement_filter_

protocols::filters::FilterOP	final_filter_

utility::vector1< MoverRealPair >	design_movers_

core::Size	explosion_

core::pack::task::TaskFactoryOP	residue_level_tasks_for_placed_hotspots_

PlacementAuctionMoverOP	auction_

protocols::protein_interface_design::filters::StubScoreFilterOP	stub_score_filter_
	does the pose have any active constraints? More...

PlacementMinimizationMoverOP	rbstub_minimization_

core::scoring::constraints::ConstraintCOPs	saved_coord_constraints_

Additional Inherited Members
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 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...

Protected Attributes inherited from protocols::simple_moves::DesignRepackMover
core::scoring::ScoreFunctionOP	scorefxn_repack_

core::scoring::ScoreFunctionOP	scorefxn_minimize_

bool	repack_partner1_

bool	repack_partner2_

bool	design_partner1_

bool	design_partner2_

utility::vector1< bool >	min_sc_

utility::vector1< bool >	curr_min_sc_

utility::vector1< bool >	min_rb_

utility::vector1< bool >	min_bb_

utility::vector1< bool >	curr_min_bb_

utility::vector1< bool >	curr_min_rb_

bool	min_rb_set_

bool	min_sc_set_

bool	min_bb_set_

utility::vector1< core::Size >	target_residues_

core::Real	interface_distance_cutoff_

bool	repack_non_ala_

bool	optimize_foldtree_

bool	automatic_repacking_definition_

core::pack::task::PackerTaskOP	task_

bool	use_preset_task_

utility::vector1< bool >	allowed_aas_

utility::vector1< core::Size >	prevent_repacking_

utility::vector1< core::Size >	restrict_to_repacking_

core::pack::task::TaskFactoryOP	task_factory_

bool	symmetry_

Detailed Description

choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria.

Member Typedef Documentation

typedef std::pair< simple_moves::DesignRepackMoverOP, bool > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::DesignMoverFoldTreePair

typedef std::pair< simple_moves::DesignRepackMoverOP, core::Real > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::DesignMoverRealPair

typedef std::pair< protocols::simple_moves::DesignRepackMoverOP, core::Real > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::MoverRealPair

typedef std::multimap< core::Real, std::pair< core::Size, StubsetStubPair > > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::ResidueAuction

typedef std::pair< core::Real, std::pair< core::Size, StubsetStubPair > > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::ResidueAuctionItem

typedef std::pair< protocols::hotspot_hashing::HotspotStubSetOP, protocols::hotspot_hashing::HotspotStubOP > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::StubsetStubPair

ResidueAuction is keyed by energy => we select the residue,stub,stubset combination with the best energy for each stubset,stub combination.

typedef std::pair< protocols::hotspot_hashing::HotspotStubSetOP, std::pair< protocols::hotspot_hashing::HotspotStubOP, core::Size > > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::StubSetStubPos

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::PlaceSimultaneouslyMover ( )

References auction_, design_movers_, explosion_, host_chain_, max_cb_cb_dist_, minimization_movers_, minimization_repeats_after_placement_, minimization_repeats_before_placement_, rbstub_minimization_, residue_level_tasks_for_placed_hotspots_, saved_bb_constraints_, saved_coord_constraints_, saved_stub_sets_, stub_energy_threshold_, stub_score_filter_, stub_set_filters_, and stub_sets_.

protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::~PlaceSimultaneouslyMover ( )

virtual

Member Function Documentation

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::add_coordinatecst_for_hotspot_packing ( core::pose::Pose & pose )

coordinate constraints to pose

References protocols::protein_interface_design::movers::add_coordinate_constraints(), runtime_assert, core::scoring::TR, and type.

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::apply ( core::pose::Pose & )

virtual

a dummy apply so that instantiation of this baseclass would be possible.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References core::scoring::backbone_stub_constraint, core::scoring::backbone_stub_linear_constraint, design, protocols::moves::FAIL_RETRY, protocols::moves::MS_SUCCESS, protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), and core::scoring::TR.

protocols::moves::MoverOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::clone ( ) const

virtual

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.

Implements protocols::simple_moves::DesignRepackMover.

core::pack::task::PackerTaskOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::create_task_for_allhotspot_packing ( core::pose::Pose const & pose )

setup the residue level tasks for each of the paired positions in stub_sets_. Add all rotamers from the auction results

References EX_THREE_THIRD_STEP_STDDEVS, core::chemical::num_canonical_aas, runtime_assert, core::scoring::TR, and type.

core::pack::task::PackerTaskOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::create_task_for_hotspot_packing ( core::pose::Pose const & pose )

setup the residue level tasks for each of the paired positions in stub_sets_. This sets the explosion level as well as the allowed identities at each position Note that two things happen in this function: 1) the task is modified to reflect the rotamer explosion operations. 2) residue_level_tasks_for_placed_hotspots_ is updated with these operations

References EX_THREE_THIRD_STEP_STDDEVS, core::chemical::num_canonical_aas, runtime_assert, and type.

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design ( core::pose::Pose & pose )

conducts user-specified design movers. Returns true if the energy per residue filter passes for each of the placed hotspots

wraps around the user-defined design movers. Applies coordinate constraints as specified by the user. Prevents repacking of placed hotspots

References core::pose::Pose::add_constraints(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, empty, prevent_repacking, protocols::simple_moves::DesignRepackMover::prevent_repacking(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), runtime_assert, protocols::simple_moves::DesignRepackMover::task_factory(), and core::scoring::TR.

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_cleanup ( core::pose::Pose & pose )

This should be called before failing placesimultaneously.

References core::pose::Pose::clear(), and core::scoring::TR.

protocols::moves::MoverOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::fresh_instance ( ) const

inlinevirtual

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.

Implements protocols::simple_moves::DesignRepackMover.

std::string protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::host_chain ( core::Size const host_chain )

inline

References host_chain(), and host_chain_.

Referenced by host_chain().

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all	(	core::pose::Pose &	pose,
		core::Size const	minimization_steps
	)		const

minimize simultaneously towards the placed stubs from each of the stub sets returns false if one of the filters fails

wraps around user-defined minimization movers. Note that setting up constraints should be done outside this method.

References core::scoring::backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::getScoreFunction(), protocols::protein_interface_design::movers::make_stub_scorefxn(), min_rb, MinimizeInterface(), protocols::antibody::design::no_min, core::pose::Pose::num_jump(), prevent_repacking, protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), repeat, runtime_assert, sc_min, core::pose::Pose::total_residue(), and core::scoring::TR.

bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb ( core::pose::Pose & pose ) const

minimize towards clouds of stubs made up of all the stub sets

if bb_cst score is 0 return false, o/w true

preliminary rb minimization step in the presence of strong hotspot constraints. Reports failure if pre-minimization bb_cst score is 0. Note that setting up constraints should be done outside

References core::scoring::backbone_stub_constraint, protocols::simple_filters::ScoreTypeFilter::compute(), protocols::protein_interface_design::movers::make_stub_scorefxn(), min_rb, MinimizeInterface(), protocols::antibody::design::no_min, core::pose::Pose::total_residue(), and core::scoring::TR.

bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions ( core::pose::Pose & pose )

pair each stub set with a position on the scaffold

if no mutually exclusive matches are found for all sets, return false

positions on the scaffold are auctioned to hotspot stub sets. The stubset that has a stub with the lowest constraint energy with respect to that position wins the auction. If the number of positions that are paired is less than the number of hotspot families, then failure is reported. If pairing succeeds, each of the paired positions is allowed to adopt an identity from its parent stubset that has below 0 constraint energy. Following which pack_rotamers is called with ex1, ex2, and rotamer explosion if directed by the user. Finally, each placed hotspot is tested for its total energy and for a user-defined filter. If one of these filters fails, failure is reported. Note that residues other than the lowest constraint energy identities might emerge from this process.

References protocols::simple_filters::EnergyPerResidueFilter::apply(), core::pose::Pose::clear(), core::pack::task::TaskFactory::clone(), clone(), core::scoring::coordinate_constraint, distance(), numeric::xyzVector< class >::distance(), core::scoring::getScoreFunction(), core::conformation::Residue::is_protein(), j, protocols::protein_interface_design::movers::make_stub_scorefxn(), min_rb, MinimizeInterface(), protocols::moves::modify_ResId_based_object(), protocols::moves::MS_SUCCESS, protocols::antibody::design::no_min, core::pack::task::PackerTask::nonconst_residue_task(), core::pose::Pose::num_jump(), pack_rotamers(), prevent_repacking, core::pack::task::ResidueLevelTask::prevent_repacking(), core::pack::task::TaskFactory::push_back(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), core::pose::Pose::residue(), sc_min, status, core::pose::Pose::total_residue(), core::scoring::total_score, core::scoring::TR, core::pose::Pose::update_residue_neighbors(), and core::conformation::Residue::xyz().

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, basic::options::OptionKeys::hotspot::allow_proline, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::filters::TrueFilter::clone(), core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), basic::datacache::DataMap::get(), core::scoring::getScoreFunction(), basic::datacache::DataMap::has(), core::pack::task::PackerTask::initialize_from_command_line(), core::conformation::Residue::is_protein(), min_rb, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, basic::options::option, core::pack::task::PackerTask::or_include_current(), core::pack::pack_rotamers(), core::pack::task::parse_resfile(), protocols::rosetta_scripts::parse_task_operations(), core::pack::task::ResidueLevelTask::prevent_repacking(), basic::options::OptionKeys::packing::resfile, core::pose::Pose::residue(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), restype, runtime_assert, core::pose::Pose::total_residue(), core::scoring::TR, user, and utility_exit_with_message.

bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs ( core::pose::Pose & pose ) const

will be removed

this will be removed in the future

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::replace_residue(), core::conformation::Conformation::update_polymeric_connection(), and core::pose::Pose::update_residue_neighbors().

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints	(	core::pose::Pose &	pose,
		core::Real const	coord_sdev
	)

removes and reinstates coordinate constraints for all placed hotspots according to coord_sdev

removes the coordinate constraints from the pose and reapplies them individually.

References core::pose::Pose::add_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), and core::scoring::TR.

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::stub_sets ( utility::vector1< StubSetStubPos > const sets )

inline

References stub_sets_.

Member Data Documentation

protocols::filters::FilterOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::after_placement_filter_

private

PlacementAuctionMoverOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::auction_

private

Referenced by PlaceSimultaneouslyMover().

core::Real protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::coor_cst_cutoff_

private

utility::vector1< MoverRealPair > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design_movers_

private

Referenced by PlaceSimultaneouslyMover().

core::Size protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::explosion_

private

Referenced by PlaceSimultaneouslyMover().

protocols::filters::FilterOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_filter_

private

core::Size protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::host_chain_

private

where is the stub to be placed

Referenced by host_chain(), and PlaceSimultaneouslyMover().

core::Real protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::max_cb_cb_dist_

private

the maximum distance for a stub to be considered a a neighbour to a host residue

Referenced by PlaceSimultaneouslyMover().

utility::vector1< MoverRealPair > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimization_movers_

private

Referenced by PlaceSimultaneouslyMover().

core::Size protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimization_repeats_after_placement_

private

Referenced by PlaceSimultaneouslyMover().

core::Size protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimization_repeats_before_placement_

private

Referenced by PlaceSimultaneouslyMover().

PlacementMinimizationMoverOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::rbstub_minimization_

private

Referenced by PlaceSimultaneouslyMover().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::residue_level_tasks_for_placed_hotspots_

private

This task factory is used by placesimultaneously in two ways: 1) internally to create a packer task for hotspot placement and user-defined design movers. 2) For design movers downstream of PlaceSimultaneously so that they are aware of the choices made by PlaceSimultaneously. Note that item 1 is not implemented in PlaceStub. This means that PlaceSimultaneously always uses the task factory, whereas PlaceStub only uses it if the user specifies TaskAware design movers.

Referenced by PlaceSimultaneouslyMover().

core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::saved_bb_constraints_

private

Referenced by PlaceSimultaneouslyMover().

core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::saved_coord_constraints_

private

Referenced by PlaceSimultaneouslyMover().

core::pose::Pose protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::saved_pose_

private

utility::vector1< StubSetStubPos > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::saved_stub_sets_

private

Referenced by PlaceSimultaneouslyMover().

core::Real protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::stub_energy_threshold_

private

Maximum per-residue energy the placed stub can have to be saved.

Referenced by PlaceSimultaneouslyMover().

protocols::protein_interface_design::filters::StubScoreFilterOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::stub_score_filter_

private

does the pose have any active constraints?

Referenced by PlaceSimultaneouslyMover().

std::map< protocols::hotspot_hashing::HotspotStubSetOP, protocols::filters::FilterOP > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::stub_set_filters_

private

Referenced by PlaceSimultaneouslyMover().

utility::vector1< StubSetStubPos > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::stub_sets_

private

stub sets and placed positions

Referenced by PlaceSimultaneouslyMover(), and stub_sets().

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

symlinks/rosetta/src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMover.hh
symlinks/rosetta/src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMover.cc

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