#include <RingConformationMover.hh>

Public Member Functions
	RingConformationMover ()
	Default constructor. More...

	RingConformationMover (RingConformationMover const &object_to_copy)
	Copy constructor. More...

	RingConformationMover (core::kinematics::MoveMapOP input_movemap)
	Constructor with MoveMap input option. More...

RingConformationMover &	operator= (RingConformationMover const &object_to_copy)

virtual	~RingConformationMover ()

virtual void	show (std::ostream &output=std::cout) const
	Generate string representation of RingConformationMover for debugging purposes. More...

virtual std::string	get_name () const
	Return the name of the Mover. More...

virtual protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

virtual void	apply (core::pose::Pose &input_pose)
	Apply the corresponding move to <input_pose>. More...

core::kinematics::MoveMapCOP	movemap () const
	Get the current MoveMap. More...

void	movemap (core::kinematics::MoveMapOP new_movemap)
	Set the MoveMap. More...

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)

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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
	Inform 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
	Inform 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

Static Public Member Functions
static void	register_options ()
	Register options with the option system. More...

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. More...

Private Member Functions
void	init (core::kinematics::MoveMapOP movemap)

void	copy_data (RingConformationMover object_to_copy_to, RingConformationMover object_to_copy_from)

void	setup_residue_list (core::pose::Pose &pose)

Private Attributes
core::kinematics::MoveMapOP	movemap_

utility::vector1< core::Size >	residue_list_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

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

Based on a given MoveMap, this mover selects movable cyclic residues and flips their rings to an idealized ring conformer.

Remarks: This class is a work in progress....

Constructor & Destructor Documentation

protocols::simple_moves::RingConformationMover::RingConformationMover ( )

Default constructor.

By default, all rings within a given pose will be allowed to move.

References init().

Referenced by clone(), and fresh_instance().

protocols::simple_moves::RingConformationMover::RingConformationMover ( RingConformationMover const & object_to_copy )

Copy constructor.

References copy_data().

protocols::simple_moves::RingConformationMover::RingConformationMover ( core::kinematics::MoveMapOP input_movemap )

Constructor with MoveMap input option.

Parameters

<input_movemap> a MoveMap with desired nu torsions set to true

Remarks: Movable cyclic residues will generally be a subset of residues in the MoveMap whose nu torsions are set to true.

References init().

protocols::simple_moves::RingConformationMover::~RingConformationMover ( )

virtual

Member Function Documentation

void protocols::simple_moves::RingConformationMover::apply ( core::pose::Pose & input_pose )

virtual

Apply the corresponding move to <input_pose>.

The mover will create a list of movable residues based on the given MoveMap and select a residue from the list at random. The torsion angles of a randomly selected ring conformer will be applied to the selected residue.

Parameters

<input_pose> the structure to be moved

Remarks: a work in progess...

Implements protocols::moves::Mover.

References chemical, get_name(), core::pose::Pose::residue(), residue_list_, protocols::simple_moves::RG, core::pose::Pose::set_ring_conformation(), setup_residue_list(), show(), protocols::simple_moves::TR, and numeric::random::RandomGenerator::uniform().

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

virtual

Return a clone of the Mover object.

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.

Reimplemented from protocols::moves::Mover.

References RingConformationMover().

void protocols::simple_moves::RingConformationMover::copy_data	(	RingConformationMover	object_to_copy_to,
		RingConformationMover	object_to_copy_from
	)

private

References movemap_, and residue_list_.

Referenced by operator=(), and RingConformationMover().

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

virtual

Generates a new Mover object freshly created with the default ctor.

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.

Reimplemented from protocols::moves::Mover.

References RingConformationMover().

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

virtual

Return the name of the Mover.

Implements protocols::moves::Mover.

References protocols::moves::Mover::type().

Referenced by apply().

void protocols::simple_moves::RingConformationMover::init ( core::kinematics::MoveMapOP movemap )

private

References movemap(), movemap_, and protocols::moves::Mover::type().

Referenced by RingConformationMover().

kinematics::MoveMapCOP protocols::simple_moves::RingConformationMover::movemap ( ) const

Get the current MoveMap.

References movemap_.

Referenced by init().

void protocols::simple_moves::RingConformationMover::movemap ( core::kinematics::MoveMapOP new_movemap )

Set the MoveMap.

References movemap_.

RingConformationMover & protocols::simple_moves::RingConformationMover::operator= ( RingConformationMover const & object_to_copy )

References copy_data(), and protocols::moves::Mover::operator=().

void protocols::simple_moves::RingConformationMover::register_options ( )

static

Register options with the option system.

void protocols::simple_moves::RingConformationMover::setup_residue_list ( core::pose::Pose & pose )

private

References core::kinematics::MoveMap::get_nu(), core::chemical::ResidueType::is_cyclic(), movemap_, core::pose::Pose::residue(), residue, residue_list_, core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by apply().

void protocols::simple_moves::RingConformationMover::show ( std::ostream & output = std::cout ) const

virtual

Generate string representation of RingConformationMover for debugging purposes.

Reimplemented from protocols::moves::Mover.

References movemap_, and protocols::moves::Mover::show().

Referenced by apply(), and protocols::simple_moves::operator<<().

Member Data Documentation

core::kinematics::MoveMapOP protocols::simple_moves::RingConformationMover::movemap_

private

Referenced by copy_data(), init(), movemap(), setup_residue_list(), and show().

utility::vector1<core::Size> protocols::simple_moves::RingConformationMover::residue_list_

private

Referenced by apply(), copy_data(), and setup_residue_list().

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

symlinks/rosetta/src/protocols/simple_moves/RingConformationMover.hh
symlinks/rosetta/src/protocols/simple_moves/RingConformationMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation