#include <RNA_KIC_Sampler.hh>

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

Public Member Functions
	RNA_KIC_Sampler (core::pose::PoseOP ref_pose, core::Size const moving_suite, core::Size const chainbreak_suite, bool const is_TNA=false)

	~RNA_KIC_Sampler () override

void	init () override
	Initialization. More...

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

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

bool	not_end () const override
	Check if reach the end of rotamer list. More...

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

void	apply ()
	Apply the current rotamer to ref_pose_. More...

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

bool	closable () const
	If the chain is closable (random modeler only) 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	set_verbose (bool const setting)

void	set_extra_epsilon (bool const setting)

void	set_extra_chi (bool const setting)

void	set_sample_all_chi (bool const setting)

void	set_skip_same_pucker (bool const setting)

void	set_idealize_coord (bool const setting)

void	set_torsion_screen (bool const setting)

void	set_pucker_state (core::chemical::rna::PuckerState const setting)

void	set_base_state (core::chemical::rna::ChiState const setting)

void	set_sample_nucleoside (core::Size const setting)

void	set_bin_size (core::Real const setting)

void	set_fast (core::Real const setting)

void	set_max_tries (core::Size const setting)
	Max # of step for trying in random sampling. More...

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

	~StepWiseSampler () override

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

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

	~SamplerPlusPlus () override

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

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 Member Functions
void	get_next_valid_bb ()

	RNA_KIC_Sampler (const RNA_KIC_Sampler &)

void	operator= (const RNA_KIC_Sampler &)

Private Attributes
core::pose::PoseOP const	ref_pose_

core::Size const	moving_suite_

core::Size const	chainbreak_suite_

core::chemical::rna::PuckerState	pucker_state_

core::chemical::rna::ChiState	base_state_

core::Size	sample_nucleoside_

core::Real	bin_size_ = 20

core::Size	max_tries_ = 100

bool	verbose_ = false

bool	extra_epsilon_ = false

bool	extra_chi_ = false

bool	sample_all_chi_ = false

bool	skip_same_pucker_ = false

bool	idealize_coord_ = false

bool	torsion_screen_ = true

bool	random_chain_closed_ = true

StepWiseSamplerSizedCombOP	bb_rotamer_

RNA_KinematicCloserOP	loop_closer_

RNA_ChiStepWiseSamplerOP	chi_rotamer_

screener::RNA_TorsionScreenerOP	screener_

bool	is_TNA_ = false

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...

Constructor & Destructor Documentation

protocols::stepwise::sampler::rna::RNA_KIC_Sampler::RNA_KIC_Sampler	(	core::pose::PoseOP	ref_pose,
		core::Size const	moving_suite,
		core::Size const	chainbreak_suite,
		bool const	is_TNA = `false`
	)

References protocols::stepwise::sampler::StepWiseSampler::set_random().

protocols::stepwise::sampler::rna::RNA_KIC_Sampler::~RNA_KIC_Sampler ( )

overridedefault

protocols::stepwise::sampler::rna::RNA_KIC_Sampler::RNA_KIC_Sampler ( const RNA_KIC_Sampler & )

private

Member Function Documentation

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply ( core::pose::Pose & pose )

overridevirtual

Apply the current rotamer to pose.

Implements protocols::toolbox::SamplerPlusPlus.

References base_state_, bb_rotamer_, chi_rotamer_, protocols::toolbox::SamplerPlusPlus::is_init(), loop_closer_, core::chemical::rna::NO_CHI, protocols::stepwise::sampler::StepWiseSampler::random(), random_chain_closed_, and protocols::stepwise::sampler::rna::TR().

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply ( )

Apply the current rotamer to ref_pose_.

References ref_pose_.

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::closable ( ) const

inline

If the chain is closable (random modeler only)

References random_chain_closed_.

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

overridevirtual

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

References chainbreak_suite_, moving_suite_, and core::id::to_string().

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::get_next_valid_bb ( )

private

References core::pose::rna::assign_pucker(), base_state_, bb_rotamer_, chainbreak_suite_, chi_rotamer_, loop_closer_, moving_suite_, core::chemical::rna::NO_CHI, ref_pose_, screener_, and torsion_screen_.

Referenced by operator++(), and reset().

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

overridevirtual

Initialization.

Implements protocols::toolbox::SamplerPlusPlus.

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::not_end ( ) const

overridevirtual

Check if reach the end of rotamer list.

Reimplemented from protocols::stepwise::sampler::StepWiseSampler.

References bb_rotamer_, and protocols::toolbox::SamplerPlusPlus::is_init().

Referenced by operator++(), and reset().

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator++ ( )

overridevirtual

Move to next rotamer.

Implements protocols::toolbox::SamplerPlusPlus.

References base_state_, bb_rotamer_, chainbreak_suite_, chi_rotamer_, get_next_valid_bb(), loop_closer_, max_tries_, moving_suite_, core::chemical::rna::NO_CHI, not_end(), protocols::stepwise::sampler::StepWiseSampler::random(), random_chain_closed_, ref_pose_, screener_, torsion_screen_, and protocols::stepwise::sampler::rna::TR().

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator= ( const RNA_KIC_Sampler & )

private

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::reset ( void )

overridevirtual

Reset to the first (or random if is_random()) rotamer.

Implements protocols::toolbox::SamplerPlusPlus.

References bb_rotamer_, get_next_valid_bb(), protocols::toolbox::SamplerPlusPlus::is_init(), loop_closer_, not_end(), protocols::stepwise::sampler::StepWiseSampler::random(), and ref_pose_.

Referenced by set_random().

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_base_state ( core::chemical::rna::ChiState const setting )

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_bin_size ( core::Real const setting )

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_extra_chi ( bool const setting )

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_extra_epsilon ( bool const setting )

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_fast ( core::Real const setting )

inline

References bin_size_, extra_chi_, extra_epsilon_, sample_all_chi_, and protocols::toolbox::SamplerPlusPlus::set_and_reinit().

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

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_max_tries ( core::Size const setting )

inline

Max # of step for trying in random sampling.

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_pucker_state ( core::chemical::rna::PuckerState const setting )

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_random ( bool const setting )

overridevirtual

Set the random modeler state.

Reimplemented from protocols::stepwise::sampler::StepWiseSampler.

References base_state_, bb_rotamer_, chi_rotamer_, protocols::toolbox::SamplerPlusPlus::is_init(), loop_closer_, core::chemical::rna::NO_CHI, reset(), and protocols::stepwise::sampler::StepWiseSampler::set_random().

Referenced by init().

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_all_chi ( bool const setting )

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_nucleoside ( core::Size const setting )

inline

References sample_nucleoside_.

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

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_torsion_screen ( bool const setting )

inline

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_verbose ( bool const setting )

inline

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

toolbox::SamplerPlusPlusType protocols::stepwise::sampler::rna::RNA_KIC_Sampler::type ( ) const

inlineoverridevirtual

Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RNA_KIC.

Member Data Documentation

core::chemical::rna::ChiState protocols::stepwise::sampler::rna::RNA_KIC_Sampler::base_state_

private

Referenced by apply(), get_next_valid_bb(), init(), operator++(), set_base_state(), and set_random().

StepWiseSamplerSizedCombOP protocols::stepwise::sampler::rna::RNA_KIC_Sampler::bb_rotamer_

private

Referenced by apply(), get_next_valid_bb(), init(), not_end(), operator++(), reset(), and set_random().

core::Real protocols::stepwise::sampler::rna::RNA_KIC_Sampler::bin_size_ = 20

private

Referenced by init(), set_bin_size(), and set_fast().

core::Size const protocols::stepwise::sampler::rna::RNA_KIC_Sampler::chainbreak_suite_

private

Referenced by get_name(), get_next_valid_bb(), init(), and operator++().

RNA_ChiStepWiseSamplerOP protocols::stepwise::sampler::rna::RNA_KIC_Sampler::chi_rotamer_

private

Referenced by apply(), get_next_valid_bb(), init(), operator++(), and set_random().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::extra_chi_ = false

private

Referenced by init(), set_extra_chi(), and set_fast().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::extra_epsilon_ = false

private

Referenced by init(), set_extra_epsilon(), and set_fast().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::idealize_coord_ = false

private

Referenced by init(), and set_idealize_coord().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::is_TNA_ = false

private

Referenced by init().

RNA_KinematicCloserOP protocols::stepwise::sampler::rna::RNA_KIC_Sampler::loop_closer_

private

Referenced by apply(), get_next_valid_bb(), init(), operator++(), reset(), and set_random().

core::Size protocols::stepwise::sampler::rna::RNA_KIC_Sampler::max_tries_ = 100

private

Referenced by operator++(), and set_max_tries().

core::Size const protocols::stepwise::sampler::rna::RNA_KIC_Sampler::moving_suite_

private

Referenced by get_name(), get_next_valid_bb(), init(), and operator++().

core::chemical::rna::PuckerState protocols::stepwise::sampler::rna::RNA_KIC_Sampler::pucker_state_

private

Referenced by init(), and set_pucker_state().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::random_chain_closed_ = true

private

Referenced by apply(), closable(), and operator++().

core::pose::PoseOP const protocols::stepwise::sampler::rna::RNA_KIC_Sampler::ref_pose_

private

Referenced by apply(), get_next_valid_bb(), init(), operator++(), and reset().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::sample_all_chi_ = false

private

Referenced by init(), set_fast(), and set_sample_all_chi().

core::Size protocols::stepwise::sampler::rna::RNA_KIC_Sampler::sample_nucleoside_

private

Referenced by init(), and set_sample_nucleoside().

screener::RNA_TorsionScreenerOP protocols::stepwise::sampler::rna::RNA_KIC_Sampler::screener_

private

Referenced by get_next_valid_bb(), and operator++().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::skip_same_pucker_ = false

private

Referenced by init(), and set_skip_same_pucker().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::torsion_screen_ = true

private

Referenced by get_next_valid_bb(), operator++(), and set_torsion_screen().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::verbose_ = false

private

Referenced by init(), and set_verbose().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation