#include <RNA_MC_Sugar.hh>

Public Member Functions
	RNA_MC_Sugar (core::Size const rsd_id, core::Real const flip_rate=0.1, PuckerState const init_pucker=NORTH)

void	init ()
	Initialization. More...

void	reset ()
	Reset to current angle. More...

void	operator++ ()
	Generate new active DOFs. More...

void	update ()
	Update the stored DOFs. More...

void	apply (core::pose::Pose &pose)
	Apply DOFs to pose. More...

void	set_flip_rate (core::Real const setting)
	Set the flip rate of pucker. More...

void	set_skip_same_pucker (bool const setting)
	Set if the sampler will skip pucker applying when input pose has. More...

void	set_idealize_coord (bool const setting)
	Set if using RNA_IdealCoord to sample puckers. More...

std::string	get_name () const
	Name of the class. More...

virtual StepWiseSamplerType	type () const
	Type of class (see enum in StepWiseSamplerTypes.hh) More...

Public Member Functions inherited from protocols::stepwise::sampler::MC_StepWiseSampler
	MC_StepWiseSampler ()

virtual	~MC_StepWiseSampler ()

virtual void	set_uniform_modeler (bool const setting)
	Set uniform modeler (instead of Gaussian) More...

virtual bool	uniform_modeler () const
	Get uniform modeler state. More...

Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerBase
	StepWiseSamplerBase ()

virtual	~StepWiseSamplerBase ()

virtual bool	not_end () const
	Check if there are more rotamers available. More...

virtual bool	random () const
	Check if is random modeler. More...

virtual void	set_random (bool const setting)
	Set the random modeler state. More...

virtual void	show (std::ostream &out, Size const indent=0) const
	output summary of class 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

void	set_type (std::string const &setting)

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 MoverOP	clone () const
	Return a clone of the Mover object. More...

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...

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

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Attributes
PuckerState	stored_pucker_state_

PuckerState	active_pucker_state_

core::Real	flip_rate_

RNA_SugarStepWiseSamplerOP	sugar_rotamer_

Additional Inherited Members
Public Types inherited from protocols::stepwise::sampler::StepWiseSamplerBase
typedef utility::vector1 < core::Real >	TorsionList

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

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...

Protected Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerBase
bool	is_init () const
	Check if the sampler has been initialized. More...

void	set_init (bool const setting)
	Set the initialization state. More...

template<class T >
void	set_and_reinit (T &params, T const &setting)
	Set value of a parameter, return to pre-init state. 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...

Constructor & Destructor Documentation

protocols::stepwise::sampler::rna::RNA_MC_Sugar::RNA_MC_Sugar	(	core::Size const	rsd_id,
		core::Real const	flip_rate = `0.1`,
		PuckerState const	init_pucker = `NORTH`
	)