#include <RNA_SugarStepWiseSampler.hh>

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

Public Member Functions
	RNA_SugarStepWiseSampler (core::Size const rsd_id, core::chemical::rna::PuckerState const pucker_state)

void	init ()
	Initialization. More...

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

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

void	set_rsd_id (core::Size const setting)
	Set the residue id being sampled. More...

core::Size const &	rsd_id () const
	Get the residue id being sampled. More...

core::chemical::rna::PuckerState	pucker () const
	Get the current pucker state. More...

void	set_pucker_state (core::chemical::rna::PuckerState const setting)
	Set the pucker_state (WHATEVER / NORTH / SOUTH) 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...

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

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

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

virtual	~StepWiseSamplerSized ()

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

Size const &	id () const

virtual void	fast_forward ()

virtual void	set_id (Size const setting)

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

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

	~StepWiseSampler ()

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 ()

virtual	~SamplerPlusPlus ()

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

	~Mover () override

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

core::Size	rsd_id_

core::chemical::rna::PuckerState	pucker_state_

bool	skip_same_pucker_

bool	idealize_coord_

std::map< core::id::DOF_ID, core::Real >	north_pucker_dof_key_values_

std::map< core::id::DOF_ID, core::Real >	south_pucker_dof_key_values_

bool	north_pucker_dofs_have_not_been_initialized_

bool	south_pucker_dofs_have_not_been_initialized_

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 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::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_SugarStepWiseSampler::RNA_SugarStepWiseSampler	(	core::Size const	rsd_id,
		core::chemical::rna::PuckerState const	pucker_state
	)

References core::chemical::rna::ANY_PUCKER, core::chemical::rna::NORTH, pucker_state_, and core::chemical::rna::SOUTH.

Member Function Documentation

void protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::apply	(	core::pose::Pose &	pose,
		core::Size const	i
	)

virtual

Apply the i-th rotamer to pose.

Implements protocols::stepwise::sampler::StepWiseSamplerSized.

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

virtual

Name of the class.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

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

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

virtual

Initialization.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References core::chemical::rna::ANY_PUCKER, core::chemical::rna::NORTH, pucker_state_, pucker_states_, protocols::stepwise::sampler::StepWiseSamplerSized::reset(), protocols::toolbox::SamplerPlusPlus::set_init(), and core::chemical::rna::SOUTH.

core::chemical::rna::PuckerState protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker ( ) const

inline

Get the current pucker state.

References protocols::stepwise::sampler::StepWiseSamplerSized::id(), protocols::toolbox::SamplerPlusPlus::is_init(), and pucker_states_.

core::Size const& protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::rsd_id ( ) const

inline

Get the residue id being sampled.

References rsd_id_.

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

inline

Set if using RNA_IdealCoord to sample puckers.

References idealize_coord_.

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

inline

Set the pucker_state (WHATEVER / NORTH / SOUTH)

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

void protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_rsd_id ( core::Size const setting )

inline

Set the residue id being sampled.

References rsd_id_.

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

inline

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

References skip_same_pucker_.

core::Size protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::size ( ) const

inlinevirtual

Get the total number of rotamers in sampler.

Implements protocols::stepwise::sampler::StepWiseSamplerSized.

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

virtual toolbox::SamplerPlusPlusType protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::type ( ) const

inlinevirtual

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

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References protocols::toolbox::RNA_SUGAR.

Member Data Documentation

bool protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::idealize_coord_

private

Referenced by apply(), and set_idealize_coord().

std::map< core::id::DOF_ID , core::Real > protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::north_pucker_dof_key_values_

private

Referenced by apply().

bool protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::north_pucker_dofs_have_not_been_initialized_

private

Referenced by apply().

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

private

Referenced by init(), RNA_SugarStepWiseSampler(), and set_pucker_state().

utility::vector1<core::chemical::rna::PuckerState> protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker_states_

private

Referenced by apply(), init(), pucker(), and size().

core::Size protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::rsd_id_

private

Referenced by apply(), get_name(), rsd_id(), and set_rsd_id().

bool protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::skip_same_pucker_

private

Referenced by apply(), and set_skip_same_pucker().

std::map< core::id::DOF_ID , core::Real > protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::south_pucker_dof_key_values_

private

Referenced by apply().

bool protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::south_pucker_dofs_have_not_been_initialized_

private

Referenced by apply().

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation