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

#include <PlaceStubMover.hh>

Inheritance diagram for protocols::protein_interface_design::movers::PlaceStubMover:

Collaboration diagram for protocols::protein_interface_design::movers::PlaceStubMover:

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

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

Public Member Functions
	PlaceStubMover ()

	PlaceStubMover (protocols::hotspot_hashing::HotspotStubSetOP stub_set, core::Real score_threshold, core::Size const host_chain, protocols::filters::FilterOP final_filter, bool const hurry=false, bool const triage_positions=true, core::Real stub_energy_threshold=1.0)

virtual	~PlaceStubMover ()

protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	stub_minimize_movers (utility::vector1< DesignMoverRealPair > const &dmrp)

utility::vector1 < DesignMoverRealPair > const &	stub_minimize_movers () const

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

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

virtual void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::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...

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
	this function informs 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
	this function informs 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

Private Member Functions
void	place_stub (core::pose::Pose &pose, core::conformation::Residue const res_stub, core::Size const res_num)

void	stub_based_atom_tree (core::pose::Pose &pose, core::conformation::Residue const res_stub, core::Real const cst_sdev)

bool	SelectStubIteratively (protocols::hotspot_hashing::HotspotStubSet::Hs_vec::const_iterator stub_it)

bool	StubMinimize (core::pose::Pose &pose, protocols::hotspot_hashing::HotspotStubCOP=NULL, core::Size const host_res=0, bool const hurry=false)

void	refresh_coordinate_constraints (core::pose::Pose &pose, core::Real const sdev)

void	cst_cleanup (core::pose::Pose &pose)
	resets pose's constraints upon stub failure remove constraints if they exist. To be used on failure More...

void	final_cleanup (core::pose::Pose &pose)
	clean everything before exiting More...

Private Attributes
core::Real	score_threshold_
	maximum bonus_value for accepting a stub More...

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

protocols::hotspot_hashing::HotspotStubSetOP	stub_set_
	stub set we're choosing from More...

bool	add_constraints_
	or use fold tree rb jump. More...

utility::vector1< core::Real >	coord_cst_std_
	what std to use for coordinate cst in each design mover More...

utility::vector1< core::Real >	disallowed_host_pos_

utility::vector1 < DesignMoverRealPair >	stub_minimize_movers_

utility::vector1 < DesignMoverFoldTreePair >	design_movers_
	utility::vector1< core::Real > coord_cst_std_stub_minimize_; More...

protocols::filters::FilterOP	after_placement_filter_
	immediately after placement + minimization More...

protocols::filters::FilterOP	final_filter_
	a filter at the last stage of placement. Defaults to TrueFilter More...

core::scoring::constraints::HarmonicFuncOP	coord_cst_func_

utility::vector1< std::pair < core::Size, bool > >	placed_stubs_

core::kinematics::FoldTreeOP	default_fold_tree_

core::scoring::constraints::ConstraintCOPs	curr_coordinate_constraints_

bool	leave_coord_csts_after_placement_

core::Real	post_placement_sdev_

core::scoring::constraints::ConstraintCOPs	previous_coordinate_constraints_

core::scoring::constraints::ConstraintCOPs	saved_bb_constraints_

utility::vector1< core::Size >	saved_prevent_repacking_

utility::vector1< std::pair < core::Size, bool > >	saved_placed_stubs_

bool	place_scaffold_
	use inverse rotamers to place the scaffold More...

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

bool	hurry_
	Should we speed up StubMinimize at the expense of accuracy? More...

bool	triage_positions_

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

core::pack::task::TaskFactoryOP	residue_level_tasks_for_placed_hotspots_

utility::pointer::owning_ptr < protocols::moves::DataMapObj < utility::vector1< core::Size > > >	residue_numbers_

std::string	user_defined_name_
	dflt NULL; a vector of residue numbers placed on the DataMap which specifies all the placed residues. Useful to communicate between movers and filters, without the pesky NotifyMovers strategy More...

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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.

Definition at line 47 of file PlaceStubMover.hh.

Member Typedef Documentation

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

Definition at line 53 of file PlaceStubMover.hh.

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

Definition at line 54 of file PlaceStubMover.hh.

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::PlaceStubMover::PlaceStubMover ( )

Definition at line 124 of file PlaceStubMover.cc.

References coord_cst_std_, curr_coordinate_constraints_, design_movers_, disallowed_host_pos_, placed_stubs_, previous_coordinate_constraints_, saved_bb_constraints_, saved_placed_stubs_, and stub_minimize_movers_.

Referenced by clone().

protocols::protein_interface_design::movers::PlaceStubMover::PlaceStubMover	(	protocols::hotspot_hashing::HotspotStubSetOP	stub_set,
		core::Real	score_threshold,
		core::Size const	host_chain,
		protocols::filters::FilterOP	final_filter,
		bool const	hurry = `false`,
		bool const	triage_positions = `true`,
		core::Real	stub_energy_threshold = `1.0`
	)

Definition at line 154 of file PlaceStubMover.cc.

References final_filter_, and stub_set_.

protocols::protein_interface_design::movers::PlaceStubMover::~PlaceStubMover ( )

virtual

Definition at line 174 of file PlaceStubMover.cc.

Member Function Documentation

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

virtual

Placing a stub in the context of a complex by putting a stub on top of the scaffold. The following steps are taken: 0. minimization of rb dofs in a bb_stub_constraint-dominated force field. Only the constraints implied by the stubset associated with this placestub mover will be applied.

stub selection, by iterating over a randomly shuffled stubset.
finding a residue on the host chain where the stub may be placed (distance cutoff).
testing the stub's repulsive energy on that residue in the context of a poly-alanine host chain.
repack/minimize the rb orientation of the pose (plus a little bb minimization around the stub, but no repacking of host_chain_).
testing the stub's total_score in the context of the full pose.
a vector of user-defined movers derived from DesignRepackMover. These may include further placestub movers. If this is the case, these movers can be constrained with coordinate constraints that are placed on the functional groups of the stub sidechain. These movers can also define the force constant of these harmonic constraints. Notice that this design should in principle be fully extensible to as many stub placement and design movers as the user chooses. If any of the user defined design movers (including subsequent stub placement) fail, another stub placement is attempted and the user defined movers are called again.
user_defined final_filter_ is called. If the pose does not pass this, place stub return to iterate over another stub. If all stubs fail, the mover signals failure and exits.

Reimplemented from protocols::simple_moves::DesignRepackMover.

Definition at line 553 of file PlaceStubMover.cc.

References core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, after_placement_filter_, protocols::protein_interface_design::movers::BuildAlaPose::apply(), core::scoring::backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), coord_cst_func_, coord_cst_std_, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), cst_cleanup(), curr_coordinate_constraints_, protocols::nonlocal::current_job(), default_fold_tree_, design_movers_, disallowed_host_pos_, core::kinematics::distance(), core::sequence::end, core::scoring::fa_rep, protocols::moves::FAIL_RETRY, final_cleanup(), final_filter_, core::pose::Pose::fold_tree(), protocols::jd2::JobDistributor::get_instance(), host_chain_, hurry_, core::pack::task::operation::PreventRepacking::include_residue(), max_cb_cb_dist_, protocols::moves::modify_ResId_based_object(), protocols::moves::MS_SUCCESS, core::conformation::Residue::name3(), place_scaffold_, place_stub(), placed_stubs_, protocols::simple_moves::DesignRepackMover::prevent_repacking(), protocols::simple_moves::DesignRepackMover::prevent_repacking_, refresh_coordinate_constraints(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::pose::Pose::residue(), residue_level_tasks_for_placed_hotspots_, residue_numbers_, protocols::rosetta_scripts::residue_packer_states(), protocols::protein_interface_design::movers::RG(), saved_bb_constraints_, saved_placed_stubs_, saved_prevent_repacking_, core::scoring::SCORE12_PATCH, SelectStubIteratively(), protocols::moves::Mover::set_last_move_status(), core::io::serialization::size(), core::scoring::SOFT_REP_DESIGN_WTS, core::scoring::STANDARD_WTS, stats_TR(), stub_energy_threshold_, stub_set_, StubMinimize(), protocols::simple_moves::DesignRepackMover::task_factory(), protocols::protein_interface_design::movers::test_res_res_aln(), core::scoring::total_score, protocols::protein_interface_design::movers::TR(), TR_debug(), triage_positions_, and user_defined_name_.

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

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 177 of file PlaceStubMover.cc.

References PlaceStubMover().

void protocols::protein_interface_design::movers::PlaceStubMover::cst_cleanup ( core::pose::Pose & pose)

private

resets pose's constraints upon stub failure remove constraints if they exist. To be used on failure

reapply saved coord constraints and refresh placed_stubs and prevent_repacking Nov09 changed logic: curr_coordinate constraints are removed only

Definition at line 917 of file PlaceStubMover.cc.

References curr_coordinate_constraints_, placed_stubs_, protocols::simple_moves::DesignRepackMover::prevent_repacking_, core::pose::Pose::remove_constraints(), saved_placed_stubs_, saved_prevent_repacking_, protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), and final_cleanup().

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

private

clean everything before exiting

This should be called before exiting placestub.

Definition at line 934 of file PlaceStubMover.cc.

References core::pose::Pose::add_constraints(), cst_cleanup(), curr_coordinate_constraints_, protocols::moves::Mover::get_last_move_status(), leave_coord_csts_after_placement_, protocols::moves::MS_SUCCESS, placed_stubs_, post_placement_sdev_, protocols::simple_moves::DesignRepackMover::prevent_repacking_, previous_coordinate_constraints_, refresh_coordinate_constraints(), protocols::simple_moves::DesignRepackMover::restrict_to_repacking_, saved_bb_constraints_, and protocols::protein_interface_design::movers::TR().

Referenced by apply().

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

inlinevirtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

Definition at line 70 of file PlaceStubMover.hh.

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

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

Definition at line 910 of file PlaceStubMover.cc.

References protocols::protein_interface_design::movers::PlaceStubMoverCreator::mover_name().

void protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::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.

Definition at line 993 of file PlaceStubMover.cc.

References core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, add_constraints_, after_placement_filter_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), coord_cst_std_, core::scoring::ScoreFunctionFactory::create_score_function(), design_movers_, disallowed_host_pos_, final_filter_, protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), protocols::moves::DataMap::get(), core::pose::get_resnum_list(), protocols::moves::DataMap::has(), host_chain_, hurry_, core::conformation::Residue::is_protein(), leave_coord_csts_after_placement_, max_cb_cb_dist_, protocols::simple_moves::DesignRepackMover::min_rb(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), core::pack::task::parse_resfile(), protocols::rosetta_scripts::parse_task_operations(), place_scaffold_, post_placement_sdev_, core::pose::Pose::residue(), residue_level_tasks_for_placed_hotspots_, residue_numbers_, core::scoring::SCORE12_PATCH, score_threshold_, core::scoring::STANDARD_WTS, stub_energy_threshold_, stub_minimize_movers_, stub_set_, protocols::simple_moves::DesignRepackMover::task(), protocols::simple_moves::DesignRepackMover::task_factory(), core::pose::Pose::total_residue(), protocols::protein_interface_design::movers::TR(), triage_positions_, and user_defined_name_.

void protocols::protein_interface_design::movers::PlaceStubMover::place_stub	(	core::pose::Pose &	pose,
		core::conformation::Residue const	res_stub,
		core::Size const	res_num
	)

private

Detailed: utility function that places a stub at an acceptor position and cleans up the pose

Definition at line 184 of file PlaceStubMover.cc.

References add_constraints_, core::kinematics::FoldTree::add_edge(), core::conformation::Residue::atom_type(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), default_fold_tree_, core::pose::Pose::fold_tree(), host_chain_, core::conformation::Residue::nbr_atom(), place_scaffold_, placed_stubs_, core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::set_jump(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::split_by_chain(), stub_based_atom_tree(), core::pose::Pose::total_residue(), TR_debug(), core::conformation::Conformation::update_polymeric_connection(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply().

void protocols::protein_interface_design::movers::PlaceStubMover::refresh_coordinate_constraints	(	core::pose::Pose &	pose,
		core::Real const	sdev
	)

private

remove all coordinate constraints from pose and then reapply them, changing the HarmonicFunc's sdev to a new value Nov09 Changing of previous logic. Now, only changing the sdev associated with the coordinate constraints.

Definition at line 524 of file PlaceStubMover.cc.

References coord_cst_func_.

Referenced by apply(), and final_cleanup().

bool protocols::protein_interface_design::movers::PlaceStubMover::SelectStubIteratively ( protocols::hotspot_hashing::HotspotStubSet::Hs_vec::const_iterator stub_it)

private

selects stubs by iterating over the stub_set_. Returns the status of stub selection

Definition at line 500 of file PlaceStubMover.cc.

References score_threshold_, stub_set_, and protocols::protein_interface_design::movers::TR().

Referenced by apply().

void protocols::protein_interface_design::movers::PlaceStubMover::stub_based_atom_tree	(	core::pose::Pose &	pose,
		core::conformation::Residue const	res_stub,
		core::Real const	cst_sdev
	)

private

changes the pose's fold-tree to connect the nearest residue on the target to the stub on the scaffold. The foldtree connects the last carbon atom before the stub's functional group. That can be useful in minimization of the pose, b/c the stub's interaction with the target will not be lost due to minimization. Notice that the pose's fold tree changes in the process and so it is usually a good idea to save the old foldtree and reinstate it after minimization. Can work with multiple stubs. In that case, rb jumps are introduced between the target and each of the stubs and a cutpoint is introduced in the putative circle that has just been formed in the fold tree. Alternatively, if the current stub is to be added via a constraint, then a coordinate constraint is set up for this stub

Definition at line 972 of file PlaceStubMover.cc.

References protocols::protein_interface_design::movers::add_coordinate_constraints(), coord_cst_func_, protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), curr_coordinate_constraints_, core::pose::Pose::fold_tree(), host_chain_, placed_stubs_, and protocols::protein_interface_design::movers::TR().

Referenced by place_stub().

void protocols::protein_interface_design::movers::PlaceStubMover::stub_minimize_movers ( utility::vector1< DesignMoverRealPair > const & dmrp)

inline

Definition at line 74 of file PlaceStubMover.hh.

References stub_minimize_movers_.

utility::vector1< DesignMoverRealPair > const& protocols::protein_interface_design::movers::PlaceStubMover::stub_minimize_movers ( ) const

inline

Definition at line 79 of file PlaceStubMover.hh.

References stub_minimize_movers_.

bool protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize	(	core::pose::Pose &	pose,
		protocols::hotspot_hashing::HotspotStubCOP	stub = `NULL`,
		core::Size const	host_residue = `0`,
		bool const	hurry = `false`
	)

private

minimize the rb orientation in the presence of a strong bb_stub_constraint potential, while reducing all other attractive scores. fa_sol is also reduced to avoid blowing up the structure. Returns false if current pose has no backbone_stub_constraint score. Removes stub constraints after minimization. If more than one stub has already been placed then the jumps are held rigid during minimization If a stub is specified, then a custom-made hotspot constraint is used

Definition at line 263 of file PlaceStubMover.cc.

References core::pose::Pose::add_constraints(), core::conformation::Residue::atom_index(), core::scoring::backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::scoring::chainbreak, protocols::simple_filters::ScoreTypeFilter::compute(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::kinematics::distance(), core::sequence::end, core::scoring::fa_atr, core::scoring::fa_dun, core::scoring::fa_pair, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, host_chain_, protocols::simple_moves::DesignRepackMover::min_rb(), MinimizeInterface(), core::pose::Pose::num_jump(), placed_stubs_, protocols::simple_moves::DesignRepackMover::prevent_repacking(), protocols::simple_moves::DesignRepackMover::prevent_repacking_, core::pose::Pose::remove_constraints(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, stats_TR(), stub_minimize_movers_, stub_set_, protocols::protein_interface_design::movers::test_res_res_aln(), core::pose::Pose::total_residue(), protocols::protein_interface_design::movers::TR(), TR_debug(), and core::conformation::Residue::xyz().

Referenced by apply().

Member Data Documentation

bool protocols::protein_interface_design::movers::PlaceStubMover::add_constraints_

private

or use fold tree rb jump.

Definition at line 118 of file PlaceStubMover.hh.

Referenced by parse_my_tag(), and place_stub().

protocols::filters::FilterOP protocols::protein_interface_design::movers::PlaceStubMover::after_placement_filter_

private

immediately after placement + minimization

Definition at line 131 of file PlaceStubMover.hh.

Referenced by apply(), and parse_my_tag().

core::scoring::constraints::HarmonicFuncOP protocols::protein_interface_design::movers::PlaceStubMover::coord_cst_func_

private

Definition at line 134 of file PlaceStubMover.hh.

Referenced by apply(), refresh_coordinate_constraints(), and stub_based_atom_tree().

utility::vector1< core::Real > protocols::protein_interface_design::movers::PlaceStubMover::coord_cst_std_

private

what std to use for coordinate cst in each design mover

dflt false

Definition at line 120 of file PlaceStubMover.hh.

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

core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::movers::PlaceStubMover::curr_coordinate_constraints_

private

saves the coordinate constraints that this mover has associated with the pose. At the end of the run, they should be removed

Definition at line 144 of file PlaceStubMover.hh.

Referenced by apply(), cst_cleanup(), final_cleanup(), PlaceStubMover(), and stub_based_atom_tree().

core::kinematics::FoldTreeOP protocols::protein_interface_design::movers::PlaceStubMover::default_fold_tree_

private

this is the foldtree with which we come into the first PlaceStubMover. It will be passed between movers for the user to decide that it should be used.

Definition at line 141 of file PlaceStubMover.hh.

Referenced by apply(), and place_stub().

utility::vector1< DesignMoverFoldTreePair > protocols::protein_interface_design::movers::PlaceStubMover::design_movers_

private

utility::vector1< core::Real > coord_cst_std_stub_minimize_;

Definition at line 129 of file PlaceStubMover.hh.

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

utility::vector1< core::Real > protocols::protein_interface_design::movers::PlaceStubMover::disallowed_host_pos_

private

Locations where stubs are not allowed to be placed

Note: This is similar to DesignRepackMover::prevent_repacking() but we want to allow repacking at steps after stub placement.

Definition at line 124 of file PlaceStubMover.hh.

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

protocols::filters::FilterOP protocols::protein_interface_design::movers::PlaceStubMover::final_filter_

private

a filter at the last stage of placement. Defaults to TrueFilter

Definition at line 133 of file PlaceStubMover.hh.

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

core::Size protocols::protein_interface_design::movers::PlaceStubMover::host_chain_

private

where is the stub to be placed

Definition at line 114 of file PlaceStubMover.hh.

Referenced by apply(), parse_my_tag(), place_stub(), stub_based_atom_tree(), and StubMinimize().

bool protocols::protein_interface_design::movers::PlaceStubMover::hurry_

private

Should we speed up StubMinimize at the expense of accuracy?

Definition at line 158 of file PlaceStubMover.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::PlaceStubMover::leave_coord_csts_after_placement_

private

Definition at line 145 of file PlaceStubMover.hh.

Referenced by final_cleanup(), and parse_my_tag().

core::Real protocols::protein_interface_design::movers::PlaceStubMover::max_cb_cb_dist_

private

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

Definition at line 156 of file PlaceStubMover.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::PlaceStubMover::place_scaffold_

private

use inverse rotamers to place the scaffold

Definition at line 154 of file PlaceStubMover.hh.

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

utility::vector1< std::pair< core::Size, bool > > protocols::protein_interface_design::movers::PlaceStubMover::placed_stubs_

private

where stubs were placed and whether they use constraints. vector is necessary to maintain the order of the placed stubs

Definition at line 137 of file PlaceStubMover.hh.

Referenced by apply(), cst_cleanup(), final_cleanup(), place_stub(), PlaceStubMover(), stub_based_atom_tree(), and StubMinimize().

core::Real protocols::protein_interface_design::movers::PlaceStubMover::post_placement_sdev_

private

Definition at line 146 of file PlaceStubMover.hh.

Referenced by final_cleanup(), and parse_my_tag().

core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::movers::PlaceStubMover::previous_coordinate_constraints_

private

Definition at line 148 of file PlaceStubMover.hh.

Referenced by final_cleanup(), and PlaceStubMover().

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

private

This task factory is used by placed stubs to add prevent repacking instructions to design movers that would be invoked after PlaceStub finishes successfully. It's a way to communicate the placements that should not be changed to design movers down stream. Note that this is a different implementation than the one used in PlaceSimultaneously.

Definition at line 168 of file PlaceStubMover.hh.

Referenced by apply(), and parse_my_tag().

utility::pointer::owning_ptr< protocols::moves::DataMapObj< utility::vector1< core::Size > > > protocols::protein_interface_design::movers::PlaceStubMover::residue_numbers_

private

Definition at line 169 of file PlaceStubMover.hh.

Referenced by apply(), and parse_my_tag().

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

private

Definition at line 149 of file PlaceStubMover.hh.

Referenced by apply(), final_cleanup(), and PlaceStubMover().

utility::vector1< std::pair< core::Size, bool > > protocols::protein_interface_design::movers::PlaceStubMover::saved_placed_stubs_

private

Definition at line 151 of file PlaceStubMover.hh.

Referenced by apply(), cst_cleanup(), and PlaceStubMover().

utility::vector1< core::Size > protocols::protein_interface_design::movers::PlaceStubMover::saved_prevent_repacking_

private

Definition at line 150 of file PlaceStubMover.hh.

Referenced by apply(), and cst_cleanup().

core::Real protocols::protein_interface_design::movers::PlaceStubMover::score_threshold_

private

maximum bonus_value for accepting a stub

Definition at line 112 of file PlaceStubMover.hh.

Referenced by parse_my_tag(), and SelectStubIteratively().

core::Real protocols::protein_interface_design::movers::PlaceStubMover::stub_energy_threshold_

private

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

Definition at line 163 of file PlaceStubMover.hh.

Referenced by apply(), and parse_my_tag().

utility::vector1< DesignMoverRealPair > protocols::protein_interface_design::movers::PlaceStubMover::stub_minimize_movers_

private

movers for stub minimization, vector of pairs of movers and whether or not to apply bb constraints during the mover

Definition at line 127 of file PlaceStubMover.hh.

Referenced by parse_my_tag(), PlaceStubMover(), stub_minimize_movers(), and StubMinimize().

protocols::hotspot_hashing::HotspotStubSetOP protocols::protein_interface_design::movers::PlaceStubMover::stub_set_

private

stub set we're choosing from

Definition at line 116 of file PlaceStubMover.hh.

Referenced by apply(), parse_my_tag(), PlaceStubMover(), SelectStubIteratively(), and StubMinimize().

bool protocols::protein_interface_design::movers::PlaceStubMover::triage_positions_

private

Should we triage host positions based on smart criteria, such as current position? Leave false if partners have not already been docked.

Definition at line 161 of file PlaceStubMover.hh.

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::PlaceStubMover::user_defined_name_

private

dflt NULL; a vector of residue numbers placed on the DataMap which specifies all the placed residues. Useful to communicate between movers and filters, without the pesky NotifyMovers strategy

Definition at line 170 of file PlaceStubMover.hh.

Referenced by apply(), and parse_my_tag().

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

src/protocols/protein_interface_design/movers/PlaceStubMover.hh
src/protocols/protein_interface_design/movers/PlaceStubMover.cc

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