#include <RNA_KicSampler.hh>

Public Member Functions
	RNA_KicSampler (core::pose::PoseOP const &ref_pose, core::Size const moving_suite, core::Size const chainbreak_suite)

	~RNA_KicSampler ()

virtual void	init ()
	Initialization. More...

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

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

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

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

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

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

bool	closable () const
	If the chain is closable (random sampling only) More...

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

virtual RotamerType	type () const
	Type of class (see enum in RotamerTypes.hh) More...

void	set_verbose (bool const setting)

void	set_extra_epsilon (bool const setting)

void	set_extra_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 (PuckerState const setting)

void	set_base_state (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 samping. More...

Public Member Functions inherited from protocols::rotamer_sampler::RotamerBase
	RotamerBase ()

virtual	~RotamerBase ()

virtual bool	random () const
	Check if is random sampling. 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

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 Member Functions
void	get_next_valid_bb ()

	RNA_KicSampler (const RNA_KicSampler &)

void	operator= (const RNA_KicSampler &)

Additional Inherited Members
Public Types inherited from protocols::rotamer_sampler::RotamerBase
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::rotamer_sampler::RotamerBase
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::rotamer_sampler::rna::RNA_KicSampler::RNA_KicSampler	(	core::pose::PoseOP const &	ref_pose,
		core::Size const	moving_suite,
		core::Size const	chainbreak_suite
	)

References protocols::rotamer_sampler::RotamerBase::set_random().

protocols::rotamer_sampler::rna::RNA_KicSampler::~RNA_KicSampler ( )

protocols::rotamer_sampler::rna::RNA_KicSampler::RNA_KicSampler ( const RNA_KicSampler & )

private

Member Function Documentation

void protocols::rotamer_sampler::rna::RNA_KicSampler::apply ( core::pose::Pose & pose )

virtual

Apply the current rotamer to pose.

Implements protocols::rotamer_sampler::RotamerBase.

References base_state_, bb_rotamer_, chi_rotamer_, protocols::rotamer_sampler::RotamerBase::is_init(), loop_closer_, NO_CHI, protocols::rotamer_sampler::RotamerBase::random(), random_chain_closed_, runtime_assert, and protocols::rotamer_sampler::rna::TR.

void protocols::rotamer_sampler::rna::RNA_KicSampler::apply ( )

Apply the current rotamer to ref_pose_.

References ref_pose_.

bool protocols::rotamer_sampler::rna::RNA_KicSampler::closable ( ) const

inline

If the chain is closable (random sampling only)

std::string protocols::rotamer_sampler::rna::RNA_KicSampler::get_name ( ) const

inlinevirtual

Name of the class.

Implements protocols::rotamer_sampler::RotamerBase.

void protocols::rotamer_sampler::rna::RNA_KicSampler::get_next_valid_bb ( )

private

References assign_pucker(), base_state_, bb_rotamer_, chainbreak_suite_, chi_rotamer_, loop_closer_, moving_suite_, NO_CHI, ref_pose_, protocols::rotamer_sampler::screener::RNA_TorsionScreener::screen(), screener_, and torsion_screen_.

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

void protocols::rotamer_sampler::rna::RNA_KicSampler::init ( void )

virtual

bool protocols::rotamer_sampler::rna::RNA_KicSampler::not_end ( ) const

virtual

Check if reach the end of rotamer list.

Reimplemented from protocols::rotamer_sampler::RotamerBase.

References bb_rotamer_, protocols::rotamer_sampler::RotamerBase::is_init(), and runtime_assert.

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

void protocols::rotamer_sampler::rna::RNA_KicSampler::operator++ ( )

virtual

Move to next rotamer.

Implements protocols::rotamer_sampler::RotamerBase.

References base_state_, bb_rotamer_, chainbreak_suite_, chi_rotamer_, get_next_valid_bb(), loop_closer_, max_tries_, moving_suite_, NO_CHI, not_end(), protocols::rotamer_sampler::RotamerBase::random(), random_chain_closed_, ref_pose_, runtime_assert, protocols::rotamer_sampler::screener::RNA_TorsionScreener::screen(), screener_, torsion_screen_, and protocols::rotamer_sampler::rna::TR.

void protocols::rotamer_sampler::rna::RNA_KicSampler::operator= ( const RNA_KicSampler & )

private

void protocols::rotamer_sampler::rna::RNA_KicSampler::reset ( void )

virtual

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

Implements protocols::rotamer_sampler::RotamerBase.

References bb_rotamer_, get_next_valid_bb(), protocols::rotamer_sampler::RotamerBase::is_init(), loop_closer_, not_end(), protocols::rotamer_sampler::RotamerBase::random(), ref_pose_, and runtime_assert.

Referenced by set_random().

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_base_state ( ChiState const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_bin_size ( core::Real const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_extra_chi ( bool const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_extra_epsilon ( bool const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_fast ( core::Real const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_idealize_coord ( bool const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_max_tries ( core::Size const setting )

inline

Max # of step for trying in random samping.

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_pucker_state ( PuckerState const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_random ( bool const setting )

virtual

Set the random sampling state.

Reimplemented from protocols::rotamer_sampler::RotamerBase.

References base_state_, bb_rotamer_, chi_rotamer_, protocols::rotamer_sampler::RotamerBase::is_init(), loop_closer_, NO_CHI, reset(), and protocols::rotamer_sampler::RotamerBase::set_random().

Referenced by init().

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_sample_nucleoside ( core::Size const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_skip_same_pucker ( bool const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_torsion_screen ( bool const setting )

inline

void protocols::rotamer_sampler::rna::RNA_KicSampler::set_verbose ( bool const setting )

inline

virtual RotamerType protocols::rotamer_sampler::rna::RNA_KicSampler::type ( ) const

inlinevirtual

Type of class (see enum in RotamerTypes.hh)

Implements protocols::rotamer_sampler::RotamerBase.

References protocols::rotamer_sampler::RNA_KIC.

Member Data Documentation

ChiState protocols::rotamer_sampler::rna::RNA_KicSampler::base_state_

private

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

RotamerSizedCombOP protocols::rotamer_sampler::rna::RNA_KicSampler::bb_rotamer_

private

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

core::Real protocols::rotamer_sampler::rna::RNA_KicSampler::bin_size_

private

Referenced by init().

core::Size const protocols::rotamer_sampler::rna::RNA_KicSampler::chainbreak_suite_

private

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

RNA_ChiRotamerOP protocols::rotamer_sampler::rna::RNA_KicSampler::chi_rotamer_

private

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

bool protocols::rotamer_sampler::rna::RNA_KicSampler::extra_chi_

private

Referenced by init().

bool protocols::rotamer_sampler::rna::RNA_KicSampler::extra_epsilon_

private

Referenced by init().

bool protocols::rotamer_sampler::rna::RNA_KicSampler::idealize_coord_

private

Referenced by init().

RNA_KinematicCloserOP protocols::rotamer_sampler::rna::RNA_KicSampler::loop_closer_

private

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

core::Size protocols::rotamer_sampler::rna::RNA_KicSampler::max_tries_

private

Referenced by operator++().

core::Size const protocols::rotamer_sampler::rna::RNA_KicSampler::moving_suite_

private

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

PuckerState protocols::rotamer_sampler::rna::RNA_KicSampler::pucker_state_

private

Referenced by init().

bool protocols::rotamer_sampler::rna::RNA_KicSampler::random_chain_closed_

private

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

core::pose::PoseOP const protocols::rotamer_sampler::rna::RNA_KicSampler::ref_pose_

private

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

core::Size protocols::rotamer_sampler::rna::RNA_KicSampler::sample_nucleoside_

private

Referenced by init().

screener::RNA_TorsionScreenerOP protocols::rotamer_sampler::rna::RNA_KicSampler::screener_

private

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

bool protocols::rotamer_sampler::rna::RNA_KicSampler::skip_same_pucker_

private

Referenced by init().

bool protocols::rotamer_sampler::rna::RNA_KicSampler::torsion_screen_

private

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

bool protocols::rotamer_sampler::rna::RNA_KicSampler::verbose_

private

Referenced by init().

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

symlinks/rosetta/src/protocols/rotamer_sampler/rna/RNA_KicSampler.hh
symlinks/rosetta/src/protocols/rotamer_sampler/rna/RNA_KicSampler.cc

Private Attributes
core::pose::PoseOP const	ref_pose_

core::Size const	moving_suite_

core::Size const	chainbreak_suite_

PuckerState	pucker_state_

ChiState	base_state_

core::Size	sample_nucleoside_

core::Real	bin_size_

core::Size	max_tries_

bool	verbose_

bool	extra_epsilon_

bool	extra_chi_

bool	skip_same_pucker_

bool	idealize_coord_

bool	torsion_screen_

bool	random_chain_closed_

RotamerSizedCombOP	bb_rotamer_

RNA_KinematicCloserOP	loop_closer_

RNA_ChiRotamerOP	chi_rotamer_

screener::RNA_TorsionScreenerOP	screener_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation