#include <RotamerRecoveryMover.hh>

Inheritance diagram for protocols::rotamer_recovery::RotamerRecoveryMover:

Collaboration diagram for protocols::rotamer_recovery::RotamerRecoveryMover:

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

	RotamerRecoveryMover (rotamer_recovery::RotamerRecoveryOP rotamer_recovery, core::scoring::ScoreFunctionOP scfxn, core::pack::task::TaskFactoryOP task_factory)

	~RotamerRecoveryMover ()

	RotamerRecoveryMover (RotamerRecoveryMover const &src)

virtual void	register_options () const

virtual void	apply (core::pose::Pose &pose)

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

virtual moves::MoverOP	clone () const
	make a copy More...

virtual moves::MoverOP	fresh_instance () const
	make a copy but use default constructor More...

virtual void	parse_my_tag (TagPtr const , moves::DataMap &, Filters_map const &, moves::Movers_map const &movers, Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...

core::scoring::ScoreFunctionOP	score_function ()

void	score_function (core::scoring::ScoreFunctionOP)

virtual void	show ()

virtual void	show (std::ostream &out)

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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Attributes
rotamer_recovery::RotamerRecoveryOP	rotamer_recovery_

core::scoring::ScoreFunctionOP	scfxn_

core::pack::task::TaskFactoryOP	task_factory_

Additional Inherited Members
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

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

Definition at line 44 of file RotamerRecoveryMover.hh.

Constructor & Destructor Documentation

protocols::rotamer_recovery::RotamerRecoveryMover::RotamerRecoveryMover ( )

default constructor

Definition at line 138 of file RotamerRecoveryMover.cc.

References task_factory_.

Referenced by clone(), and fresh_instance().

protocols::rotamer_recovery::RotamerRecoveryMover::RotamerRecoveryMover	(	rotamer_recovery::RotamerRecoveryOP	rotamer_recovery,
		core::scoring::ScoreFunctionOP	scfxn,
		core::pack::task::TaskFactoryOP	task_factory
	)

protocols::rotamer_recovery::RotamerRecoveryMover::~RotamerRecoveryMover ( )

Definition at line 156 of file RotamerRecoveryMover.cc.

protocols::rotamer_recovery::RotamerRecoveryMover::RotamerRecoveryMover ( RotamerRecoveryMover const & src)

Definition at line 158 of file RotamerRecoveryMover.cc.

Member Function Documentation

void protocols::rotamer_recovery::RotamerRecoveryMover::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 199 of file RotamerRecoveryMover.cc.

References rotamer_recovery_, score_function(), and task_factory_.

MoverOP protocols::rotamer_recovery::RotamerRecoveryMover::clone ( ) const

virtual

make a copy

Reimplemented from protocols::moves::Mover.

Definition at line 220 of file RotamerRecoveryMover.cc.

References RotamerRecoveryMover().

MoverOP protocols::rotamer_recovery::RotamerRecoveryMover::fresh_instance ( ) const

virtual

make a copy but use default constructor

Reimplemented from protocols::moves::Mover.

Definition at line 214 of file RotamerRecoveryMover.cc.

References RotamerRecoveryMover().

string protocols::rotamer_recovery::RotamerRecoveryMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 209 of file RotamerRecoveryMover.cc.

void protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag	(	TagPtr const	tag,
		moves::DataMap &	data,
		Filters_map const &	filters,
		moves::Movers_map const &	movers,
		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::moves::Mover.

Definition at line 225 of file RotamerRecoveryMover.cc.

References protocols::moves::DataMap::get(), protocols::rotamer_recovery::RotamerRecoveryFactory::get_instance(), protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_comparer(), protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_protocol(), protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_reporter(), protocols::rosetta_scripts::parse_mover(), rotamer_recovery_, score_function(), and protocols::rotamer_recovery::TR().

void protocols::rotamer_recovery::RotamerRecoveryMover::register_options ( ) const

virtual

Definition at line 168 of file RotamerRecoveryMover.cc.

References rotamer_recovery_.

bool protocols::rotamer_recovery::RotamerRecoveryMover::reinitialize_for_each_job ( ) const

virtual

this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use.

Reimplemented from protocols::moves::Mover.

Definition at line 189 of file RotamerRecoveryMover.cc.

bool protocols::rotamer_recovery::RotamerRecoveryMover::reinitialize_for_new_input ( ) const

virtual

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).

Reimplemented from protocols::moves::Mover.

Definition at line 194 of file RotamerRecoveryMover.cc.

ScoreFunctionOP protocols::rotamer_recovery::RotamerRecoveryMover::score_function ( )

Definition at line 266 of file RotamerRecoveryMover.cc.

References core::scoring::getScoreFunction(), and scfxn_.

Referenced by apply(), and parse_my_tag().

void protocols::rotamer_recovery::RotamerRecoveryMover::score_function ( core::scoring::ScoreFunctionOP )

void protocols::rotamer_recovery::RotamerRecoveryMover::show ( )

virtual

Definition at line 281 of file RotamerRecoveryMover.cc.

References rotamer_recovery_.

void protocols::rotamer_recovery::RotamerRecoveryMover::show ( std::ostream & out)

virtual

Definition at line 286 of file RotamerRecoveryMover.cc.

References rotamer_recovery_.

Member Data Documentation

rotamer_recovery::RotamerRecoveryOP protocols::rotamer_recovery::RotamerRecoveryMover::rotamer_recovery_

private

Definition at line 126 of file RotamerRecoveryMover.hh.

Referenced by apply(), parse_my_tag(), register_options(), and show().

core::scoring::ScoreFunctionOP protocols::rotamer_recovery::RotamerRecoveryMover::scfxn_

private

Definition at line 127 of file RotamerRecoveryMover.hh.

Referenced by score_function().

core::pack::task::TaskFactoryOP protocols::rotamer_recovery::RotamerRecoveryMover::task_factory_

private

Definition at line 128 of file RotamerRecoveryMover.hh.

Referenced by apply(), and RotamerRecoveryMover().

The documentation for this class was generated from the following files:

src/protocols/rotamer_recovery/RotamerRecoveryMover.hh
src/protocols/rotamer_recovery/RotamerRecoveryMover.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation