#include <RNA_MC_Suite.hh>

Inheritance diagram for protocols::stepwise::sampler::rna::RNA_MC_Suite:

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

void	init ()
	Initialization. More...

void	clear_rotamer ()
	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_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...

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_Comb
	MC_Comb ()

virtual	~MC_Comb ()

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

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

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

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

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

virtual void	add_external_loop_rotamer (MC_StepWiseSamplerOP const &rotamer)
	Add one more rotamer sampler to this sampler. More...

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

virtual	~MC_StepWiseSampler ()

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 ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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...

virtual 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
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	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< RNA_MC_SugarOP >	sugar_samplers_

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

Member Function Documentation

void protocols::stepwise::sampler::rna::RNA_MC_Suite::clear_rotamer ( )

virtual

Clear all rotamer samplers stored in this sampler.

Reimplemented from protocols::stepwise::sampler::MC_Comb.

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

Referenced by init().

std::string protocols::stepwise::sampler::rna::RNA_MC_Suite::get_name ( ) const

inlinevirtual

Name of the class.

Reimplemented from protocols::stepwise::sampler::MC_Comb.

void protocols::stepwise::sampler::rna::RNA_MC_Suite::init ( void )

virtual

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_a_form_range ( core::Real const setting )

inline

Set angle ranges for A form rotamers.

References a_form_range_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit().

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_gaussian_stdev ( core::Real const setting )

Set the standard deviation of Gaussian sampler.

References bb_samplers_, chi_samplers_, gaussian_stdev_, and protocols::stepwise::sampler::StepWiseSamplerBase::is_init().

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_idealize_coord ( bool const setting )

inline

Set if using RNA_IdealCoord to sample puckers.

References idealize_coord_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit().

void protocols::stepwise::sampler::rna::RNA_MC_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::stepwise::sampler::StepWiseSamplerBase::set_init(), core::pose::Pose::torsion(), and torsion_ids_.

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

inline

Set starting torsions and pucker states.

References init_pucker_, init_torsions_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_init().

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_pucker_flip_rate ( core::Real const setting )

Set the flip rate of pucker.

References protocols::stepwise::sampler::StepWiseSamplerBase::is_init(), pucker_flip_rate_, and sugar_samplers_.

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_sample_bb ( bool const setting )

inline

Set if sample backbone.

References sample_bb_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit().

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_sample_lower_nucleoside ( bool const setting )

inline

Set if sample nucleoside.

References sample_lower_nucleoside_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit().

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_sample_near_a_form ( bool const setting )

inline

Set if only sample near A form rotamers.

References sample_near_a_form_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit().

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_sample_upper_nucleoside ( bool const setting )

inline

Set if sample nucleoside.

References sample_upper_nucleoside_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit().

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_skip_same_pucker ( bool const setting )

inline

Set if the sampler will skip pucker applying when input pose has.

References protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit(), and skip_same_pucker_.

virtual StepWiseSamplerType protocols::stepwise::sampler::rna::RNA_MC_Suite::type ( ) const

inlinevirtual

Type of class (see enum in StepWiseSamplerTypes.hh)

Implements protocols::stepwise::sampler::StepWiseSamplerBase.

References protocols::stepwise::sampler::RNA_MC_SUITE.

Member Data Documentation

core::Real protocols::stepwise::sampler::rna::RNA_MC_Suite::a_form_range_

private

Referenced by init(), and set_a_form_range().

utility::vector1<core::Real> protocols::stepwise::sampler::rna::RNA_MC_Suite::a_form_torsions_

private

Referenced by init(), and RNA_MC_Suite().

utility::vector1<MC_OneTorsionOP> protocols::stepwise::sampler::rna::RNA_MC_Suite::bb_samplers_

private

Referenced by clear_rotamer(), init(), and set_gaussian_stdev().

utility::vector1<MC_OneTorsionOP> protocols::stepwise::sampler::rna::RNA_MC_Suite::chi_samplers_

private

Referenced by clear_rotamer(), init(), and set_gaussian_stdev().

core::Real protocols::stepwise::sampler::rna::RNA_MC_Suite::gaussian_stdev_

private

Referenced by init(), and set_gaussian_stdev().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::idealize_coord_

private

Referenced by init(), and set_idealize_coord().

core::chemical::rna::PuckerState protocols::stepwise::sampler::rna::RNA_MC_Suite::init_pucker_

private

Referenced by init(), set_init_from_pose(), and set_init_states().

utility::vector1<core::Real> protocols::stepwise::sampler::rna::RNA_MC_Suite::init_torsions_

private

Referenced by init(), RNA_MC_Suite(), set_init_from_pose(), and set_init_states().

core::Real protocols::stepwise::sampler::rna::RNA_MC_Suite::pucker_flip_rate_

private

Referenced by init(), and set_pucker_flip_rate().

core::Size const protocols::stepwise::sampler::rna::RNA_MC_Suite::rsd_id_

private

Referenced by init(), and set_init_from_pose().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::sample_bb_

private

Referenced by init(), and set_sample_bb().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::sample_lower_nucleoside_

private

Referenced by init(), and set_sample_lower_nucleoside().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::sample_near_a_form_

private

Referenced by init(), and set_sample_near_a_form().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::sample_upper_nucleoside_

private

Referenced by init(), and set_sample_upper_nucleoside().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::skip_same_pucker_

private

Referenced by init(), and set_skip_same_pucker().

utility::vector1<RNA_MC_SugarOP> protocols::stepwise::sampler::rna::RNA_MC_Suite::sugar_samplers_

private

Referenced by clear_rotamer(), init(), and set_pucker_flip_rate().

utility::vector1<core::id::TorsionID> protocols::stepwise::sampler::rna::RNA_MC_Suite::torsion_ids_

private

Referenced by init(), RNA_MC_Suite(), and set_init_from_pose().

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

src/protocols/stepwise/sampler/rna/RNA_MC_Suite.hh
src/protocols/stepwise/sampler/rna/RNA_MC_Suite.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation