#include <MC_RNA_Sugar.hh>

Inheritance diagram for protocols::recces::sampler::rna::MC_RNA_Sugar:

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

void	init () override
	Initialization. More...

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

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

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

void	apply (core::pose::Pose &pose) override
	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 override
	Name of the class. More...

toolbox::SamplerPlusPlusType	type () const override
	Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh) More...

void	show (std::ostream &out, core::Size const indent) const override
	output summary of class More...

MC_SamplerOP	find (core::id::TorsionID const &torsion_id) override
	return OP to the subsampler that controls exactly this torsion_id (assume only one). More...

Public Member Functions inherited from protocols::recces::sampler::MC_Sampler
	MC_Sampler ()

	~MC_Sampler () override

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...

virtual void	set_update_pose (core::pose::PoseCOP setting)
	set (optional) update_pose More...

bool	found_move () const
	check if ++ did anything to pose. More...

void	set_name (std::string const &setting)
	Set name of the class. More...

void	restore (core::pose::Pose &)
	restore pose to state prior to this sampler's apply(). Would enable big speedup in monte carlo by obviating pose copies. More...

Public Member Functions inherited from protocols::toolbox::SamplerPlusPlus
	SamplerPlusPlus ()

	~SamplerPlusPlus () override

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

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

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

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

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes
core::chemical::rna::PuckerState	stored_pucker_state_

core::chemical::rna::PuckerState	active_pucker_state_

core::Real	flip_rate_

stepwise::sampler::rna::RNA_SugarStepWiseSamplerOP	sugar_rotamer_

Additional Inherited Members
Public Types inherited from protocols::toolbox::SamplerPlusPlus
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 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::toolbox::SamplerPlusPlus
bool	is_init () const
	return OP to the subsampler that controls exactly this torsion_id (assume only one). This is worked out in recces/sampler/MC_Sampler & derived classes – wouldn't be too hard to generalize to stepwise/sampler/ classes, too. 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...

Protected Attributes inherited from protocols::recces::sampler::MC_Sampler
bool	found_move_
	used to prevent simulated tempering from counting move if its filtered out. More...

PoseCOP	update_pose_
	optional: pose accumulating changes in markov chain monte carlo, can use for updating sampler. More...

std::string	name_

Constructor & Destructor Documentation

protocols::recces::sampler::rna::MC_RNA_Sugar::MC_RNA_Sugar	(	core::Size const	rsd_id,
		core::Real const	flip_rate = `0.1`,
		core::chemical::rna::PuckerState const	init_pucker = `core::chemical::rna::NORTH`
	)