a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing. More...

#include <MinPackMover.hh>

Inheritance diagram for protocols::simple_moves::MinPackMover:

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Collaboration diagram for protocols::simple_moves::MinPackMover:

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Public Types
typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

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

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
	MinPackMover ()
	default constructor More...

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

	MinPackMover (ScoreFunctionCOP scorefxn)

	MinPackMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task)

virtual	~MinPackMover ()

	MinPackMover (MinPackMover const &other)

void	init ()

virtual void	apply (Pose &pose)

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

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

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	score_function (ScoreFunctionCOP sf)

void	task_factory (TaskFactoryCOP tf)

void	task (PackerTaskCOP t)

ScoreFunctionCOP	score_function () const

PackerTaskCOP	task () const

TaskFactoryCOP	task_factory () const

void	stochastic_pack (bool)

bool	stochastic_pack () 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_

PackerTaskCOP	task_

TaskFactoryCOP	task_factory_

bool	stochastic_pack_

bool	nonideal_

bool	cartesian_

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 mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing.

Definition at line 45 of file MinPackMover.hh.

Member Typedef Documentation

typedef core::pack::task::PackerTaskCOP protocols::simple_moves::MinPackMover::PackerTaskCOP

Definition at line 47 of file MinPackMover.hh.

typedef core::scoring::ScoreFunctionCOP protocols::simple_moves::MinPackMover::ScoreFunctionCOP

Definition at line 49 of file MinPackMover.hh.

typedef core::pack::task::TaskFactoryCOP protocols::simple_moves::MinPackMover::TaskFactoryCOP

Definition at line 48 of file MinPackMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::MinPackMover::MinPackMover ( )

default constructor

Definition at line 78 of file MinPackMover.cc.

References init().

Referenced by fresh_instance().

protocols::simple_moves::MinPackMover::MinPackMover ( std::string const & type_name)

constructor with typename

Definition at line 88 of file MinPackMover.cc.

References init().

protocols::simple_moves::MinPackMover::MinPackMover ( ScoreFunctionCOP scorefxn)

Definition at line 99 of file MinPackMover.cc.

References init().

protocols::simple_moves::MinPackMover::MinPackMover	(	ScoreFunctionCOP	scorefxn,
		PackerTaskCOP	task
	)

Definition at line 112 of file MinPackMover.cc.

References init().

protocols::simple_moves::MinPackMover::~MinPackMover ( )

virtual

Definition at line 125 of file MinPackMover.cc.

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

Definition at line 134 of file MinPackMover.cc.

References cartesian_, nonideal_, score_function(), scorefxn_, task(), task_, task_factory(), and task_factory_.

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Definition at line 147 of file MinPackMover.cc.

References cartesian_, core::scoring::ScoreFunctionFactory::create_score_function(), core::pack::min_pack(), nonideal_, scorefxn_, core::scoring::STANDARD_WTS, core::pack::stochastic_pack(), stochastic_pack_, task(), task_, task_factory_, and task_is_valid().

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 255 of file MinPackMover.cc.

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 248 of file MinPackMover.cc.

References MinPackMover().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 174 of file MinPackMover.cc.

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

void protocols::simple_moves::MinPackMover::init ( void )

Definition at line 128 of file MinPackMover.cc.

References cartesian_, and nonideal_.

Referenced by MinPackMover().

void protocols::simple_moves::MinPackMover::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 192 of file MinPackMover.cc.

References cartesian_, nonideal_, parse_score_function(), parse_task_operations(), and protocols::simple_moves::TR().

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

virtual

parse "scorefxn" XML option (can be employed virtually by derived Packing movers)

Definition at line 218 of file MinPackMover.cc.

References protocols::rosetta_scripts::parse_score_function(), and score_function().

Referenced by parse_my_tag().

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

virtual

parse "task_operations" XML option (can be employed virtually by derived Packing movers)

Definition at line 233 of file MinPackMover.cc.

References protocols::rosetta_scripts::parse_task_operations(), and task_factory().

Referenced by parse_my_tag().

void protocols::simple_moves::MinPackMover::score_function ( ScoreFunctionCOP sf)

Definition at line 262 of file MinPackMover.cc.

References scorefxn_.

Referenced by MinPackMover().

ScoreFunctionCOP protocols::simple_moves::MinPackMover::score_function ( ) const

Definition at line 277 of file MinPackMover.cc.

References scorefxn_.

Referenced by parse_score_function().

void protocols::simple_moves::MinPackMover::stochastic_pack ( bool setting)

Definition at line 281 of file MinPackMover.cc.

References stochastic_pack_.

bool protocols::simple_moves::MinPackMover::stochastic_pack ( ) const

Definition at line 282 of file MinPackMover.cc.

References stochastic_pack_.

void protocols::simple_moves::MinPackMover::task ( PackerTaskCOP t)

Referenced by MinPackMover().

PackerTaskCOP protocols::simple_moves::MinPackMover::task ( ) const

Definition at line 278 of file MinPackMover.cc.

References task_.

Referenced by apply().

void protocols::simple_moves::MinPackMover::task_factory ( TaskFactoryCOP tf)

Definition at line 270 of file MinPackMover.cc.

References task_factory_.

Referenced by MinPackMover().

TaskFactoryCOP protocols::simple_moves::MinPackMover::task_factory ( ) const

Definition at line 279 of file MinPackMover.cc.

References task_factory_.

Referenced by parse_task_operations().

bool protocols::simple_moves::MinPackMover::task_is_valid ( Pose const & pose) const

when the PackerTask was not generated locally, verify compatibility with pose

the pose residue types must be equivalent to the ones used to generate the ResidueLevelTasks, because of the way that prevent_repacking and its associated flags work

Definition at line 181 of file MinPackMover.cc.

References core::pose::Pose::residue_type(), task_, and core::pose::Pose::total_residue().

Referenced by apply().