#include <MC_RNA_Suite.hh>

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

Public Member Functions
	MC_RNA_Suite (core::Size const rsd_id)

void	init () override
	Initialization. More...

void	clear_rotamer () override
	Clear all rotamer samplers stored in this sampler. More...

void	set_gaussian_stdev (core::Real const setting)
	Set the standard deviation of Gaussian sampler. More...

void	set_angle_range_from_init (core::Real const setting)
	Set the angle range from the initial torsions. More...

void	set_pucker_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...

void	set_a_form_range (core::Real const setting)
	Set angle ranges for A form rotamers. More...

void	set_sample_near_a_form (bool const setting)
	Set if only sample near A form rotamers. More...

void	set_sample_bb (bool const setting)
	Set if sample backbone. More...

void	set_sample_lower_nucleoside (bool const setting)
	Set if sample nucleoside. More...

void	set_sample_upper_nucleoside (bool const setting)
	Set if sample nucleoside. More...

void	set_init_states (utility::vector1< core::Real > const &init_torsions, core::chemical::rna::PuckerState const init_pucker)
	Set starting torsions and pucker states. More...

void	set_init_from_pose (core::pose::Pose const &pose)
	Set starting torsions and pucker states from pose. More...

void	set_angle (core::pose::Pose const &pose)
	Set the stored angle from a pose. 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...

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

	~MC_Comb () override

void	reset () override
	Reset to the first (or random if random()) rotamer. More...

void	operator++ () override
	Move to next rotamer. More...

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

void	apply (core::pose::Pose &pose) override
	Apply the current rotamer to pose. More...

void	set_uniform_modeler (bool const setting) override
	Get uniform modeler state. More...

virtual void	add_rotamer (MC_SamplerOP const &rotamer)
	Add one more rotamer sampler to this sampler. More...

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

void	show (std::ostream &out, core::Size const indent=0) 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...

core::Size	num_rotamers () const

MC_SamplerOP	operator[] (core::Size const id)

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

	~MC_Sampler () override

virtual bool	uniform_modeler () const
	Get uniform modeler state. 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::Size const	rsd_id_

bool	skip_same_pucker_

bool	idealize_coord_

bool	sample_near_a_form_

bool	sample_bb_

bool	sample_lower_nucleoside_

bool	sample_upper_nucleoside_

core::Real	pucker_flip_rate_

core::Real	gaussian_stdev_

core::Real	angle_range_

core::Real	a_form_range_

core::chemical::rna::PuckerState	init_pucker_

utility::vector1< core::Real >	a_form_torsions_

utility::vector1< core::Real >	init_torsions_

utility::vector1 < core::id::TorsionID >	torsion_ids_

utility::vector1< MC_OneTorsionOP >	bb_samplers_

utility::vector1< MC_OneTorsionOP >	chi_samplers_

utility::vector1< MC_RNA_SugarOP >	sugar_samplers_

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_Comb
utility::vector1< MC_SamplerOP >	rotamer_list_

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_Suite::MC_RNA_Suite ( core::Size const rsd_id )

Member Function Documentation

void protocols::recces::sampler::rna::MC_RNA_Suite::clear_rotamer ( )

overridevirtual

Clear all rotamer samplers stored in this sampler.

Reimplemented from protocols::recces::sampler::MC_Comb.

References bb_samplers_, chi_samplers_, protocols::recces::sampler::MC_Comb::clear_rotamer(), and sugar_samplers_.

Referenced by init().

std::string protocols::recces::sampler::rna::MC_RNA_Suite::get_name ( ) const

inlineoverridevirtual

Name of the class.

Reimplemented from protocols::recces::sampler::MC_Sampler.

void protocols::recces::sampler::rna::MC_RNA_Suite::init ( void )

overridevirtual

void protocols::recces::sampler::rna::MC_RNA_Suite::set_a_form_range ( core::Real const setting )

inline

Set angle ranges for A form rotamers.

References a_form_range_, and protocols::toolbox::SamplerPlusPlus::set_and_reinit().

void protocols::recces::sampler::rna::MC_RNA_Suite::set_angle ( core::pose::Pose const & pose )

Set the stored angle from a pose.

References bb_samplers_, chi_samplers_, core::pose::Pose::torsion(), and torsion_ids_.

void protocols::recces::sampler::rna::MC_RNA_Suite::set_angle_range_from_init ( core::Real const setting )

Set the angle range from the initial torsions.

References angle_range_, bb_samplers_, chi_samplers_, init_torsions_, and protocols::toolbox::SamplerPlusPlus::is_init().

void protocols::recces::sampler::rna::MC_RNA_Suite::set_gaussian_stdev ( core::Real const setting )

Set the standard deviation of Gaussian sampler.

References bb_samplers_, chi_samplers_, gaussian_stdev_, and protocols::toolbox::SamplerPlusPlus::is_init().

void protocols::recces::sampler::rna::MC_RNA_Suite::set_idealize_coord ( bool const setting )

inline

Set if using RNA_IdealCoord to sample puckers.

References idealize_coord_, and protocols::toolbox::SamplerPlusPlus::set_and_reinit().

void protocols::recces::sampler::rna::MC_RNA_Suite::set_init_from_pose ( core::pose::Pose const & pose )

Set starting torsions and pucker states from pose.

References core::pose::rna::assign_pucker(), init_pucker_, init_torsions_, rsd_id_, protocols::toolbox::SamplerPlusPlus::set_init(), core::pose::Pose::torsion(), and torsion_ids_.

void protocols::recces::sampler::rna::MC_RNA_Suite::set_init_states	(	utility::vector1< core::Real > const &	init_torsions,
		core::chemical::rna::PuckerState const	init_pucker
	)