saves a pose and reapplies its sequence and rotamers at a later stage. The constructor saves the initial pose, and then any calls to apply replace the residues on the input pose with that saved pose. Notice, that only ALA positions will be replaced, so this is meant to work strictly along with BuildAlaPose moves. This way, if in the design process an interface residue is designed, that will not be reverted to w/t More...

#include <SaveAndRetrieveSidechains.hh>

Inheritance diagram for protocols::protein_interface_design::movers::SaveAndRetrieveSidechains:

[legend]

Public Types
typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > >	BoolDataCacheBoolOP

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

Public Member Functions
	SaveAndRetrieveSidechains ()

	SaveAndRetrieveSidechains (core::pose::Pose const &pose, bool const allsc=false, bool const ensure_variant_matching=false, core::Size const jumpid=1)

	~SaveAndRetrieveSidechains () override

bool	allsc () const

void	allsc (bool const allsc)

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...

bool	two_step () const

void	two_step (bool const b)

bool	multi_use () const

void	multi_use (bool const b)

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...

Private Attributes
PoseCOP	init_pose_

bool	allsc_

bool	ensure_variant_matching_

bool	two_step_

bool	multi_use_

core::Size	jumpid_

BoolDataCacheBoolOP	first_apply_

Additional Inherited Members
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_

Detailed Description

saves a pose and reapplies its sequence and rotamers at a later stage. The constructor saves the initial pose, and then any calls to apply replace the residues on the input pose with that saved pose. Notice, that only ALA positions will be replaced, so this is meant to work strictly along with BuildAlaPose moves. This way, if in the design process an interface residue is designed, that will not be reverted to w/t

Member Typedef Documentation

◆ BoolDataCacheBoolOP

typedef utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > > protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::BoolDataCacheBoolOP

◆ Pose

typedef core::pose::Pose protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::Pose

◆ PoseOP

typedef core::pose::PoseOP protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::PoseOP

Constructor & Destructor Documentation

◆ SaveAndRetrieveSidechains() [1/2]

protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::SaveAndRetrieveSidechains ( )

References allsc_, ensure_variant_matching_, first_apply_, init_pose_, jumpid_, multi_use_, and two_step_.

◆ SaveAndRetrieveSidechains() [2/2]

protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::SaveAndRetrieveSidechains	(	core::pose::Pose const &	pose,
		bool const	allsc = `false`,
		bool const	ensure_variant_matching = `false`,
		core::Size const	jumpid = `1`
	)

References first_apply_, init_pose_, multi_use_, and two_step_.

◆ ~SaveAndRetrieveSidechains()

protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::~SaveAndRetrieveSidechains ( )

overridedefault

Member Function Documentation

◆ allsc() [1/2]

bool protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::allsc ( ) const

inline

References allsc_.

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and protocols::protein_interface_design::movers::LoopRemodel::apply().

◆ allsc() [2/2]

void protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::allsc ( bool const allsc )

inline

References allsc(), and allsc_.

Referenced by allsc().

◆ apply()

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

overridevirtual

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

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References core::pose::add_variant_type_to_pose_residue(), allsc_, core::pose::Pose::clone(), core::pose::Pose::conformation(), ensure_variant_matching_, first_apply_, core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueProperties::get_variant_from_string(), core::chemical::ResidueTypeBase::has_variant_type(), init_pose_, core::pose::symmetry::is_symmetric(), core::pose::Pose::jump(), jumpid_, multi_use(), core::conformation::Residue::name3(), core::chemical::ResidueTypeBase::properties(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_jump(), core::pose::Pose::size(), protocols::protein_interface_design::movers::TR(), two_step(), and core::chemical::variants_match().

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and protocols::protein_interface_design::movers::LoopRemodel::apply().

◆ clone()

protocols::moves::MoverOP protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::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()

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

inlineoverridevirtual

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::SaveAndRetrieveSidechains::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References mover_name().

◆ mover_name()

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

static

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

◆ multi_use() [1/2]

bool protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::multi_use ( ) const

inline

References multi_use_.

Referenced by apply(), and parse_my_tag().

◆ multi_use() [2/2]

void protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::multi_use ( bool const b )

inline

References protocols::match::upstream::b, and multi_use_.

◆ parse_my_tag()

void protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::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 allsc_, first_apply_, init_pose_, jumpid_, protocols::rosetta_scripts::legacy_saved_pose_or_input(), mover_name(), multi_use(), and two_step().