#include <SymPackRotamersMover.hh>

Inheritance diagram for protocols::simple_moves::symmetry::SymPackRotamersMover:

Collaboration diagram for protocols::simple_moves::symmetry::SymPackRotamersMover:

Public Member Functions
	SymPackRotamersMover ()
	PackRotamersMover. More...

	SymPackRotamersMover (core::scoring::ScoreFunctionCOP scorefxn, core::pack::task::PackerTaskCOP task=0, core::Size nloop=1)

	~SymPackRotamersMover ()

	SymPackRotamersMover (PackRotamersMover const &other)

void	make_symmetric_task (core::pose::Pose &pose, core::pack::task::PackerTaskOP task)

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

virtual protocols::moves::MoverOP	clone () const
	required in the context of the parser/scripting scheme More...

virtual protocols::moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme More...

virtual void	parse_my_tag (utility::tag::TagPtr const tag, moves::DataMap &data, filters::Filters_map const &filters, moves::Movers_map const &movers, core::pose::Pose const &pose)
	parse XML (specifically in the context of the parser/scripting scheme) More...

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

Public Member Functions inherited from protocols::simple_moves::PackRotamersMover
	PackRotamersMover ()
	default constructor More...

	PackRotamersMover (std::string const &)
	constructor with typename More...

	PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1)
	Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More...

virtual	~PackRotamersMover ()

	PackRotamersMover (PackRotamersMover const &other)

virtual void	apply (Pose &pose)
	Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More...

bool	task_is_valid (Pose const &pose) const
	when the PackerTask was not generated locally, verify compatibility with pose More...

virtual void	parse_score_function (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

virtual void	parse_task_operations (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...

void	score_function (ScoreFunctionCOP sf)
	Sets the ScoreFunction to <sf> More...

void	task_factory (TaskFactoryCOP tf)
	Sets the TaskFactory to <tf> More...

void	task (PackerTaskCOP t)
	Sets the PackerTask to <t> More...

void	nloop (core::Size nloop_in)

ScoreFunctionCOP	score_function () const
	Returns the ScoreFunction. More...

PackerTaskCOP	task () const
	Returns the PackerTask. More...

core::Size	nloop () const

TaskFactoryCOP	task_factory () const
	Returns the TaskFactory. More...

RotamerSetsCOP	rotamer_sets () const

InteractionGraphBaseCOP	ig () const

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	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
virtual void	setup (core::pose::Pose &pose)
	get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More...

virtual core::PackerEnergy	run (core::pose::Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const

Private Attributes
core::pack::rotamer_set::symmetry::SymmetricRotamerSetsOP	sym_rotamer_sets_

core::pack::task::PackerTaskOP	symmetric_task_

InteractionGraphBaseOP	symmetric_ig_

Additional Inherited Members
Public Types inherited from protocols::simple_moves::PackRotamersMover
typedef core::pack::interaction_graph::InteractionGraphBaseOP	InteractionGraphBaseOP
	please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here! More...

typedef core::pack::interaction_graph::InteractionGraphBaseCOP	InteractionGraphBaseCOP

typedef core::pack::rotamer_set::RotamerSetsOP	RotamerSetsOP

typedef core::pack::rotamer_set::RotamerSetsCOP	RotamerSetsCOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryCOP	TaskFactoryCOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

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::simple_moves::PackRotamersMover
virtual void	note_packertask_settings (Pose const &)
	note PackerTask's packable and designable residues as string info More...

Detailed Description

Definition at line 36 of file SymPackRotamersMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::symmetry::SymPackRotamersMover::SymPackRotamersMover ( )

PackRotamersMover.

Definition at line 84 of file SymPackRotamersMover.cc.

Referenced by clone(), and fresh_instance().

protocols::simple_moves::symmetry::SymPackRotamersMover::SymPackRotamersMover	(	core::scoring::ScoreFunctionCOP	scorefxn,
		core::pack::task::PackerTaskCOP	task = `0`,
		core::Size	nloop = `1`
	)

protocols::simple_moves::symmetry::SymPackRotamersMover::~SymPackRotamersMover ( )

Definition at line 100 of file SymPackRotamersMover.cc.

protocols::simple_moves::symmetry::SymPackRotamersMover::SymPackRotamersMover ( PackRotamersMover const & other)

Definition at line 102 of file SymPackRotamersMover.cc.

References sym_rotamer_sets_.

Member Function Documentation

protocols::moves::MoverOP protocols::simple_moves::symmetry::SymPackRotamersMover::clone ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 188 of file SymPackRotamersMover.cc.

References SymPackRotamersMover().

Referenced by setup().

protocols::moves::MoverOP protocols::simple_moves::symmetry::SymPackRotamersMover::fresh_instance ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 189 of file SymPackRotamersMover.cc.

References SymPackRotamersMover().

std::string protocols::simple_moves::symmetry::SymPackRotamersMover::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 126 of file SymPackRotamersMover.cc.

void protocols::simple_moves::symmetry::SymPackRotamersMover::make_symmetric_task	(	core::pose::Pose &	pose,
		core::pack::task::PackerTaskOP	task
	)

Definition at line 167 of file SymPackRotamersMover.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::conformation(), core::conformation::symmetry::is_symmetric(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

Referenced by setup().

void protocols::simple_moves::symmetry::SymPackRotamersMover::parse_def	(	utility::lua::LuaObject const &	def,
		utility::lua::LuaObject const &	score_fxns,
		utility::lua::LuaObject const &	tasks,
		protocols::moves::MoverCacheSP	cache
	)

virtual

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 203 of file SymPackRotamersMover.cc.

References protocols::simple_moves::PackRotamersMover::parse_def().

void protocols::simple_moves::symmetry::SymPackRotamersMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		moves::DataMap &	data,
		filters::Filters_map const &	filters,
		moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 193 of file SymPackRotamersMover.cc.

References protocols::simple_moves::PackRotamersMover::parse_my_tag().

core::PackerEnergy protocols::simple_moves::symmetry::SymPackRotamersMover::run	(	core::pose::Pose &	pose,
		utility::vector0< int >	rot_to_pack = `utility::vector0<int>()`
	)		const