A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains() More...

#include <RepackSidechainsMover.hh>

Inheritance diagram for protocols::simple_moves::RepackSidechainsMover:

Collaboration diagram for protocols::simple_moves::RepackSidechainsMover:

Public Types
typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

Public Member Functions
	RepackSidechainsMover ()
	default constructor More...

	RepackSidechainsMover (ScoreFunctionCOP scorefxn)
	constructor with typename More...

	RepackSidechainsMover (RepackSidechainsMover const &other)

virtual void	apply (Pose &pose)

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

virtual void	parse_my_tag (TagPtr const, protocols::moves::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse XML (specifically in the context of the parser/scripting scheme) 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 protocols::moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme More...

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

void	set_scorefxn (ScoreFunctionCOP sf)

ScoreFunctionCOP	scorefxn () 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	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
ScoreFunctionCOP	scorefxn_

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...

Detailed Description

A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains()

Definition at line 38 of file RepackSidechainsMover.hh.

Member Typedef Documentation

typedef core::scoring::ScoreFunctionCOP protocols::simple_moves::RepackSidechainsMover::ScoreFunctionCOP

Definition at line 40 of file RepackSidechainsMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::RepackSidechainsMover::RepackSidechainsMover ( )

default constructor

Definition at line 75 of file RepackSidechainsMover.cc.

Referenced by fresh_instance().

protocols::simple_moves::RepackSidechainsMover::RepackSidechainsMover ( ScoreFunctionCOP scorefxn)

constructor with typename

Constructs a RepackSidechainsMover with PackerTask <task> evaluated using <scorefxn>

ScoreFunction scorefxn /function to minimize while changine rotamers PackerTask task /object specifying what to design/pack Size (int) nloop /number of loops in the Pose (???)

Definition at line 86 of file RepackSidechainsMover.cc.

protocols::simple_moves::RepackSidechainsMover::RepackSidechainsMover ( RepackSidechainsMover const & other)

Definition at line 93 of file RepackSidechainsMover.cc.

References scorefxn(), and scorefxn_.

Member Function Documentation

void protocols::simple_moves::RepackSidechainsMover::apply ( Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 101 of file RepackSidechainsMover.cc.

References core::pack::task::TaskFactory::create_packer_task(), core::pack::figure_out_repackable_residues(), core::pose::initialize_atomid_map(), core::pack::pack_rotamers(), and scorefxn_.

protocols::moves::MoverOP protocols::simple_moves::RepackSidechainsMover::clone ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 166 of file RepackSidechainsMover.cc.

protocols::moves::MoverOP protocols::simple_moves::RepackSidechainsMover::fresh_instance ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 159 of file RepackSidechainsMover.cc.

References RepackSidechainsMover().

std::string protocols::simple_moves::RepackSidechainsMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 123 of file RepackSidechainsMover.cc.

References protocols::simple_moves::RepackSidechainsMoverCreator::mover_name().

void protocols::simple_moves::RepackSidechainsMover::parse_my_tag	(	TagPtr const	tag,
		protocols::moves::DataMap &	datamap,
		Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		Pose const &	pose
	)

virtual

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

Reimplemented from protocols::moves::Mover.

Definition at line 130 of file RepackSidechainsMover.cc.

References parse_score_function().

void protocols::simple_moves::RepackSidechainsMover::parse_score_function	(	TagPtr const	tag,
		protocols::moves::DataMap const &	datamap,
		Filters_map const &	,
		protocols::moves::Movers_map const &	,
		Pose const &
	)