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:

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Collaboration diagram for protocols::protein_interface_design::movers::SaveAndRetrieveSidechains:

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Public Types
typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

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)

virtual	~SaveAndRetrieveSidechains ()

bool	allsc () const

void	allsc (bool const allsc)

void	apply (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...

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	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 Attributes
PoseOP	init_pose_

bool	allsc_

bool	ensure_variant_matching_

core::Size	jumpid_

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

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

Definition at line 41 of file SaveAndRetrieveSidechains.hh.

Member Typedef Documentation

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

Definition at line 44 of file SaveAndRetrieveSidechains.hh.

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

Definition at line 45 of file SaveAndRetrieveSidechains.hh.

Constructor & Destructor Documentation

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

Definition at line 68 of file SaveAndRetrieveSidechains.cc.

References allsc_, ensure_variant_matching_, and jumpid_.

Referenced by clone().

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`
	)

Definition at line 76 of file SaveAndRetrieveSidechains.cc.

References init_pose_.

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

virtual

Definition at line 90 of file SaveAndRetrieveSidechains.cc.

Member Function Documentation

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

inline

Definition at line 55 of file SaveAndRetrieveSidechains.hh.

References allsc_.

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

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

inline

Definition at line 56 of file SaveAndRetrieveSidechains.hh.

References allsc(), and allsc_.

Referenced by allsc().

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

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

Definition at line 93 of file SaveAndRetrieveSidechains.cc.

References core::pose::add_variant_type_to_pose_residue(), allsc_, core::pose::Pose::conformation(), ensure_variant_matching_, core::chemical::ResidueType::has_variant_type(), init_pose_, core::pose::symmetry::is_symmetric(), core::pose::Pose::jump(), jumpid_, core::conformation::Residue::name3(), 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::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), protocols::protein_interface_design::movers::TR(), core::chemical::ResidueType::variant_types(), and core::chemical::ResidueType::variants_match().

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

protocols::moves::MoverOP protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::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 153 of file SaveAndRetrieveSidechains.cc.

References SaveAndRetrieveSidechains().

protocols::moves::MoverOP protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::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 60 of file SaveAndRetrieveSidechains.hh.

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

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

Definition at line 141 of file SaveAndRetrieveSidechains.cc.

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

void protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::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 146 of file SaveAndRetrieveSidechains.cc.

References allsc_, and init_pose_.