#include <RNA_SuiteStepWiseSampler.hh>

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

Public Member Functions
	RNA_SuiteStepWiseSampler (core::Size const rsd_id, core::chemical::rna::PuckerState const pucker_state_lower, core::chemical::rna::PuckerState const pucker_state_upper, core::chemical::rna::ChiState const base_state_lower, core::chemical::rna::ChiState const base_state_upper, bool tna_lower=false, bool tna_upper=false)

void	init () override
	Initialization wrapper. More...

void	init_standard ()
	Initialization for standard modeler. More...

void	init_fast ()
	Initialization for fast mode. More...

void	set_sample_nucleoside_lower (bool const setting)
	Set functions. More...

void	set_sample_nucleoside_upper (bool const setting)

void	set_extra_epsilon (bool const setting)

void	set_extra_beta (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_fast (bool const setting)
	Fast mode: just sample popular center torsions. More...

void	set_bin_size (core::Real const setting)

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::stepwise::sampler::StepWiseSamplerSizedAny
	StepWiseSamplerSizedAny ()

	~StepWiseSamplerSizedAny () override

void	init () override
	Initialization. More...

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

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

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

void	apply (core::pose::Pose &pose, core::Size const i) override
	Apply the i-th rotamer to pose. More...

core::Size	size () const override
	Get the total number of rotamers in sampler. More...

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

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

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

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

void	show (std::ostream &out, core::Size const indent=0) const override
	output summary of class More...

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

	~StepWiseSamplerSized () override

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

core::Size const &	id () const

virtual void	fast_forward ()

virtual void	set_id (core::Size const setting)

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

	~StepWiseSampler () override

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

virtual void	set_random (bool const setting)
	Set the random modeler state. 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 Member Functions
TorsionList	fast_sample_torsions_from_info (utility::vector1< core::chemical::rna::GaussianParameter > const &params)

Private Attributes
core::Size const	rsd_id_

core::chemical::rna::ChiState	base_state_lower_

core::chemical::rna::ChiState	base_state_upper_

bool	tna_lower_ = false

bool	tna_upper_ = false

bool	sample_nucleoside_lower_ = true

bool	sample_nucleoside_upper_ = true

bool	extra_epsilon_ = false

bool	extra_beta_ = false

bool	extra_chi_ = false

bool	sample_all_chi_ = false

bool	skip_same_pucker_ = true

bool	idealize_coord_ = true

bool	fast_ = false

core::Real	bin_size_ = 20

utility::vector1 < core::chemical::rna::PuckerState >	pucker_states_lower_

utility::vector1 < core::chemical::rna::PuckerState >	pucker_states_upper_

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::stepwise::sampler::StepWiseSamplerSized
core::Size	id_

Constructor & Destructor Documentation

protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::RNA_SuiteStepWiseSampler	(	core::Size const	rsd_id,
		core::chemical::rna::PuckerState const	pucker_state_lower,
		core::chemical::rna::PuckerState const	pucker_state_upper,
		core::chemical::rna::ChiState const	base_state_lower,
		core::chemical::rna::ChiState const	base_state_upper,
		bool	tna_lower = `false`,
		bool	tna_upper = `false`
	)

References core::chemical::rna::ANY_PUCKER, core::chemical::rna::NORTH, pucker_states_lower_, pucker_states_upper_, and core::chemical::rna::SOUTH.

Member Function Documentation

RNA_SuiteStepWiseSampler::TorsionList protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::fast_sample_torsions_from_info ( utility::vector1< core::chemical::rna::GaussianParameter > const & params )

private

References core::conformation::membrane::center.

Referenced by init_fast().

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

overridevirtual

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

References rsd_id_, and core::id::to_string().

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

overridevirtual

Initialization wrapper.

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::stepwise::sampler::StepWiseSamplerSizedAny::clear_rotamer(), fast_, protocols::stepwise::sampler::StepWiseSamplerSizedAny::init(), init_fast(), init_standard(), pucker_states_lower_, pucker_states_upper_, sample_nucleoside_lower_, and sample_nucleoside_upper_.

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_fast ( )

Initialization for fast mode.

Referenced by init().

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard ( )

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

inline

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

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_beta ( bool const setting )

inline

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

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

inline

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

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

inline

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

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_fast ( bool const setting )

inline

Fast mode: just sample popular center torsions.

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

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

inline

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

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::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_SuiteStepWiseSampler::set_sample_nucleoside_lower ( bool const setting )

inline

Set functions.

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

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_sample_nucleoside_upper ( bool const setting )

inline

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

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

inline

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

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

inlineoverridevirtual

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RNA_SUITE.

Member Data Documentation

core::chemical::rna::ChiState protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::base_state_lower_

private

Referenced by init_fast(), and init_standard().

core::chemical::rna::ChiState protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::base_state_upper_

private

Referenced by init_fast(), and init_standard().

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

private

Referenced by init_standard(), and set_bin_size().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::extra_beta_ = false

private

Referenced by init_fast(), init_standard(), and set_extra_beta().

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

private

Referenced by init_fast(), init_standard(), and set_extra_chi().

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

private

Referenced by init_fast(), init_standard(), and set_extra_epsilon().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::fast_ = false

private

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

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::idealize_coord_ = true

private

Referenced by init_fast(), init_standard(), and set_idealize_coord().

utility::vector1<core::chemical::rna::PuckerState> protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::pucker_states_lower_

private

Referenced by init(), init_fast(), init_standard(), and RNA_SuiteStepWiseSampler().

utility::vector1<core::chemical::rna::PuckerState> protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::pucker_states_upper_

private

Referenced by init(), init_fast(), init_standard(), and RNA_SuiteStepWiseSampler().

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

private

Referenced by get_name(), init_fast(), and init_standard().

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

private

Referenced by init_standard(), and set_sample_all_chi().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::sample_nucleoside_lower_ = true

private

Referenced by init(), init_fast(), init_standard(), and set_sample_nucleoside_lower().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::sample_nucleoside_upper_ = true

private

Referenced by init(), init_fast(), init_standard(), and set_sample_nucleoside_upper().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::skip_same_pucker_ = true

private

Referenced by init_fast(), init_standard(), and set_skip_same_pucker().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::tna_lower_ = false

private

Referenced by init_standard().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::tna_upper_ = false

private

Referenced by init_standard().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation