#include <PlaceOnLoop.hh>

Inheritance diagram for protocols::protein_interface_design::movers::PlaceOnLoop:

[legend]

Public Member Functions
	PlaceOnLoop ()

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

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

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

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

void	set_kinematic_defaults ()

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

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

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

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

bool	loop_length (core::pose::Pose &pose)

	~PlaceOnLoop () override

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

Public Member Functions inherited from protocols::calc_taskop_movers::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 (core::select::residue_selector::ResidueSelectorOP min_sc)

utility::vector1< bool >	min_sc (core::pose::Pose const &pose) const

bool	min_sc_set () const

void	min_bb (core::select::residue_selector::ResidueSelectorOP min_bb)

utility::vector1< bool >	min_bb (core::pose::Pose const &pose) 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

	~DesignRepackMover () override

void	target_residues (core::select::residue_selector::ResidueSelectorCOP setting)
	Replace the current target_residue setting with the passed residue selector. More...

core::select::residue_selector::ResidueSelectorCOP	target_residues () const

utility::vector1< core::Size >	target_residues (core::pose::Pose const &pose) const

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

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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

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

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

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

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

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

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

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

std::string	get_type () const

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

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

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

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

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

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

jobdist::BasicJobCOP	get_current_job () const

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

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

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

virtual core::Real	last_proposal_density_ratio ()

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

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

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

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

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

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

Static Public Member Functions inherited from protocols::calc_taskop_movers::DesignRepackMover
static utility::tag::XMLSchemaComplexTypeGeneratorOP	get_xsd_complex_type ()

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...

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

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

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::calc_taskop_movers::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_rb_

utility::vector1< bool >	curr_min_sc_

utility::vector1< bool >	curr_min_bb_

utility::vector1< bool >	curr_min_rb_

bool	min_rb_set_

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_

Constructor & Destructor Documentation

◆ PlaceOnLoop()

protocols::protein_interface_design::movers::PlaceOnLoop::PlaceOnLoop ( )

References delta_length_, kinematic_mover_, and set_kinematic_defaults().

◆ ~PlaceOnLoop()

protocols::protein_interface_design::movers::PlaceOnLoop::~PlaceOnLoop ( )

overridedefault

Member Function Documentation

◆ add_bb_csts_to_loop()

void protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop ( core::pose::Pose & pose ) const

bb_csts only affect loop. Transforms loop to poly-ala

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::aa_pro, core::conformation::Residue::atom_index(), core::pack::task::TaskFactory::create_packer_task(), curr_loop_end_, host_chain_, core::pose::Pose::residue(), core::pose::Pose::size(), and stub_set_.

Referenced by loop_length().

◆ ala_pose_loop()

void protocols::protein_interface_design::movers::PlaceOnLoop::ala_pose_loop ( core::pose::Pose & pose ) const

References core::chemical::aa_ala, core::pack::task::TaskFactory::create_packer_task(), curr_loop_end_, hires_scorefxn_, loop_begin_, core::chemical::num_canonical_aas, core::pack::pack_rotamers(), and core::pose::Pose::size().

Referenced by loop_length().

◆ apply()

void protocols::protein_interface_design::movers::PlaceOnLoop::apply ( Pose & )

overridevirtual

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

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::chemical::modifications::FAIL_RETRY, host_chain_, loop_begin_, loop_end_, loop_length(), protocols::moves::MS_SUCCESS, and protocols::moves::Mover::set_last_move_status().

◆ clone()

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

overridevirtual

Return a clone of the Mover object.

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

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

MoverOP protocols::protein_interface_design::movers::PlaceOnLoop::fresh_instance ( ) const

overridevirtual

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

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

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

overridevirtual

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

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References mover_name().

◆ loop_length()

bool protocols::protein_interface_design::movers::PlaceOnLoop::loop_length ( core::pose::Pose & pose )

Chooses one user-defined loop length at random, changes the loop accordingly, and tries to close the loop with that change.

References core::chemical::aa_from_oneletter_code(), add_bb_csts_to_loop(), ala_pose_loop(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), curr_loop_end_, core::pose::Pose::delete_polymer_residue(), delta_length_, core::pose::get_restype_for_pose(), loop_begin_, loop_end_, minimize_toward_stub(), minimize_toward_stub_, core::chemical::name_from_aa(), position_stub(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::scoring::rg, core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), and parse_my_tag().

◆ minimize_toward_stub()

bool protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub ( core::pose::Pose & pose ) const

References protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), chain_closing_attempts_, protocols::loops::Loop::choose_cutpoint(), curr_loop_end_, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::moves::Mover::get_last_move_status(), hires_scorefxn_, kinematic_mover_, loop_begin_, protocols::moves::MS_SUCCESS, protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_task_factory(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by loop_length().

◆ mover_name()

std::string protocols::protein_interface_design::movers::PlaceOnLoop::mover_name ( )

static

Referenced by get_name(), protocols::protein_interface_design::movers::PlaceOnLoopCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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

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

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References chain_closing_attempts_, delta_length_, hires_scorefxn_, host_chain_, loop_begin_, loop_end_, loop_length(), lores_scorefxn_, minimize_toward_stub_, core::scoring::parse_score_function(), stub_set_, and protocols::protein_interface_design::movers::TR().

◆ position_stub()

bool protocols::protein_interface_design::movers::PlaceOnLoop::position_stub ( core::pose::Pose & pose ) const

Referenced by loop_length().

◆ provide_xml_schema()

void protocols::protein_interface_design::movers::PlaceOnLoop::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::protein_interface_design::movers::PlaceOnLoopCreator::provide_xml_schema().

◆ set_kinematic_defaults()

void protocols::protein_interface_design::movers::PlaceOnLoop::set_kinematic_defaults ( )

set the defaults for the kinmover. Taken from Jacob's LoopRemodel

References hires_scorefxn_, and kinematic_mover_.

Referenced by PlaceOnLoop().

Member Data Documentation

◆ chain_closing_attempts_

core::Size protocols::protein_interface_design::movers::PlaceOnLoop::chain_closing_attempts_

private

Referenced by minimize_toward_stub(), and parse_my_tag().

◆ curr_loop_end_

core::Size protocols::protein_interface_design::movers::PlaceOnLoop::curr_loop_end_

private

Referenced by add_bb_csts_to_loop(), ala_pose_loop(), loop_length(), and minimize_toward_stub().

◆ delta_length_

utility::vector1< int > protocols::protein_interface_design::movers::PlaceOnLoop::delta_length_

private

Referenced by loop_length(), parse_my_tag(), and PlaceOnLoop().

◆ hires_scorefxn_

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::PlaceOnLoop::hires_scorefxn_

private

Referenced by ala_pose_loop(), minimize_toward_stub(), parse_my_tag(), and set_kinematic_defaults().

◆ host_chain_

core::Size protocols::protein_interface_design::movers::PlaceOnLoop::host_chain_

private

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

◆ kinematic_mover_

protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP protocols::protein_interface_design::movers::PlaceOnLoop::kinematic_mover_

private

Referenced by minimize_toward_stub(), PlaceOnLoop(), and set_kinematic_defaults().

◆ loop_begin_

core::Size protocols::protein_interface_design::movers::PlaceOnLoop::loop_begin_

private

Referenced by ala_pose_loop(), apply(), loop_length(), minimize_toward_stub(), and parse_my_tag().

◆ loop_end_

core::Size protocols::protein_interface_design::movers::PlaceOnLoop::loop_end_

private

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

◆ lores_scorefxn_

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::PlaceOnLoop::lores_scorefxn_

private

Referenced by parse_my_tag().

◆ minimize_toward_stub_

bool protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub_

private

Referenced by loop_length(), and parse_my_tag().

◆ stub_set_

protocols::hotspot_hashing::HotspotStubSetOP protocols::protein_interface_design::movers::PlaceOnLoop::stub_set_

private

Referenced by add_bb_csts_to_loop(), and parse_my_tag().

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

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

Private Attributes
core::Size	loop_begin_

core::Size	loop_end_

core::Size	curr_loop_end_

core::scoring::ScoreFunctionOP	hires_scorefxn_

core::scoring::ScoreFunctionOP	lores_scorefxn_

utility::vector1< int >	delta_length_

core::Size	chain_closing_attempts_

core::Size	host_chain_

protocols::hotspot_hashing::HotspotStubSetOP	stub_set_

bool	minimize_toward_stub_

protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP	kinematic_mover_

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ PlaceOnLoop()

◆ ~PlaceOnLoop()

Member Function Documentation

◆ add_bb_csts_to_loop()

◆ ala_pose_loop()

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ loop_length()

◆ minimize_toward_stub()

◆ mover_name()

◆ parse_my_tag()

◆ position_stub()

◆ provide_xml_schema()

◆ set_kinematic_defaults()

Member Data Documentation

◆ chain_closing_attempts_

◆ curr_loop_end_

◆ delta_length_

◆ hires_scorefxn_

◆ host_chain_

◆ kinematic_mover_

◆ loop_begin_

◆ loop_end_

◆ lores_scorefxn_

◆ minimize_toward_stub_

◆ stub_set_