#include <RNA_TorsionMover.hh>

Inheritance diagram for protocols::swa::monte_carlo::RNA_TorsionMover:

Collaboration diagram for protocols::swa::monte_carlo::RNA_TorsionMover:

Public Member Functions
	~RNA_TorsionMover ()

virtual void	apply (core::pose::Pose &pose_to_visualize)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	apply (core::pose::Pose &pose, std::string &move_type, Real const &sample_range)

void	random_torsion_move (pose::Pose &pose, utility::vector1< Size > const &moving_res_list, std::string &move_type, Real const &sample_range)

void	sample_near_suite_torsion (utility::vector1< Real > &torsion_list, Real const stddev)

void	sample_near_nucleoside_torsion (utility::vector1< Real > &torsion_list, Real const stddev)

void	apply_random_nucleoside_torsion (pose::Pose &pose, Size const moving_res)

void	apply_random_suite_torsion (pose::Pose &pose, Size const moving_suite)

void	apply_nucleoside_torsion_Aform (pose::Pose &pose, Size const moving_res)

void	apply_suite_torsion_Aform (pose::Pose &pose, Size const moving_suite)

void	sample_near_suite_torsion (pose::Pose &pose, Size const moving_suite, Real const sample_range)

void	sample_near_nucleoside_torsion (pose::Pose &pose, Size const moving_res, Real const sample_range)

void	crankshaft_alpha_gamma (pose::Pose &pose, Size const moving_suite, Real const sample_range)

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
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, 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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	apply_nucleoside_torsion (utility::vector1< Real > const &torsion_set, pose::Pose &pose, Size const moving_res)

void	apply_suite_torsion (utility::vector1< Real > const &torsion_set, pose::Pose &pose, Size const moving_suite)

utility::vector1< Real >	get_suite_torsion (pose::Pose const &pose, Size const moving_suite)

utility::vector1< Real >	get_nucleoside_torsion (pose::Pose const &pose, Size const moving_nucleoside)

Private Attributes
Size	default_sample_range_

core::scoring::rna::RNA_FittedTorsionInfo	rna_fitted_torsion_info_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 35 of file RNA_TorsionMover.hh.

Constructor & Destructor Documentation

protocols::swa::monte_carlo::RNA_TorsionMover::~RNA_TorsionMover ( )

Definition at line 65 of file RNA_TorsionMover.cc.

Member Function Documentation

void protocols::swa::monte_carlo::RNA_TorsionMover::apply ( core::pose::Pose & pose_to_visualize)

virtual

Implements protocols::moves::Mover.

Definition at line 70 of file RNA_TorsionMover.cc.

void protocols::swa::monte_carlo::RNA_TorsionMover::apply	(	core::pose::Pose &	pose,
		std::string &	move_type,
		Real const &	sample_range
	)

Definition at line 79 of file RNA_TorsionMover.cc.

References protocols::swa::monte_carlo::SubToFullInfo::moving_res_list(), and protocols::swa::monte_carlo::nonconst_sub_to_full_info_from_pose().

void protocols::swa::monte_carlo::RNA_TorsionMover::apply_nucleoside_torsion	(	utility::vector1< Real > const &	torsion_set,
		pose::Pose &	pose,
		Size const	moving_res
	)

private

Definition at line 197 of file RNA_TorsionMover.cc.

References core::id::BB, core::id::CHI, and core::pose::Pose::set_torsion().

void protocols::swa::monte_carlo::RNA_TorsionMover::apply_nucleoside_torsion_Aform	(	pose::Pose &	pose,
		Size const	moving_res
	)

Definition at line 302 of file RNA_TorsionMover.cc.

void protocols::swa::monte_carlo::RNA_TorsionMover::apply_random_nucleoside_torsion	(	pose::Pose &	pose,
		Size const	moving_res
	)

Definition at line 241 of file RNA_TorsionMover.cc.

References core::scoring::rna::is_purine(), core::pose::Pose::residue(), and core::conformation::symmetry::RG().

void protocols::swa::monte_carlo::RNA_TorsionMover::apply_random_suite_torsion	(	pose::Pose &	pose,
		Size const	moving_suite
	)

Definition at line 266 of file RNA_TorsionMover.cc.

References core::pose::Pose::delta(), and core::conformation::symmetry::RG().

void protocols::swa::monte_carlo::RNA_TorsionMover::apply_suite_torsion	(	utility::vector1< Real > const &	torsion_set,
		pose::Pose &	pose,
		Size const	moving_suite
	)

private

Definition at line 223 of file RNA_TorsionMover.cc.

References core::id::BB, and core::pose::Pose::set_torsion().

void protocols::swa::monte_carlo::RNA_TorsionMover::apply_suite_torsion_Aform	(	pose::Pose &	pose,
		Size const	moving_suite
	)

Definition at line 315 of file RNA_TorsionMover.cc.

void protocols::swa::monte_carlo::RNA_TorsionMover::crankshaft_alpha_gamma	(	pose::Pose &	pose,
		Size const	moving_suite,
		Real const	sample_range
	)

Definition at line 375 of file RNA_TorsionMover.cc.

References core::id::BB, core::conformation::symmetry::RG(), core::pose::Pose::set_torsion(), and core::pose::Pose::torsion().

std::string protocols::swa::monte_carlo::RNA_TorsionMover::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Definition at line 154 of file RNA_TorsionMover.cc.

utility::vector1< Real > protocols::swa::monte_carlo::RNA_TorsionMover::get_nucleoside_torsion	(	pose::Pose const &	pose,
		Size const	moving_nucleoside
	)

private

Definition at line 347 of file RNA_TorsionMover.cc.

References core::id::BB, core::id::CHI, and core::pose::Pose::torsion().

utility::vector1< Real > protocols::swa::monte_carlo::RNA_TorsionMover::get_suite_torsion	(	pose::Pose const &	pose,
		Size const	moving_suite
	)

private

Definition at line 331 of file RNA_TorsionMover.cc.

References core::id::BB, and core::pose::Pose::torsion().

void protocols::swa::monte_carlo::RNA_TorsionMover::random_torsion_move	(	pose::Pose &	pose,
		utility::vector1< Size > const &	moving_res_list,
		std::string &	move_type,
		Real const &	sample_range
	)

Definition at line 88 of file RNA_TorsionMover.cc.

References protocols::swa::monte_carlo::CHAIN_TERMINUS_3PRIME, protocols::swa::monte_carlo::CHAIN_TERMINUS_5PRIME, protocols::swa::monte_carlo::get_moving_residue_case(), protocols::swa::monte_carlo::INTERNAL, and core::conformation::symmetry::RG().

void protocols::swa::monte_carlo::RNA_TorsionMover::sample_near_nucleoside_torsion	(	utility::vector1< Real > &	torsion_list,
		Real const	stddev
	)

Definition at line 178 of file RNA_TorsionMover.cc.

References core::conformation::symmetry::RG().

void protocols::swa::monte_carlo::RNA_TorsionMover::sample_near_nucleoside_torsion	(	pose::Pose &	pose,
		Size const	moving_res,
		Real const	sample_range
	)

Definition at line 368 of file RNA_TorsionMover.cc.

void protocols::swa::monte_carlo::RNA_TorsionMover::sample_near_suite_torsion	(	utility::vector1< Real > &	torsion_list,
		Real const	stddev
	)

Definition at line 161 of file RNA_TorsionMover.cc.

References core::conformation::symmetry::RG().

void protocols::swa::monte_carlo::RNA_TorsionMover::sample_near_suite_torsion	(	pose::Pose &	pose,
		Size const	moving_suite,
		Real const	sample_range
	)

Definition at line 360 of file RNA_TorsionMover.cc.

Member Data Documentation

Size protocols::swa::monte_carlo::RNA_TorsionMover::default_sample_range_

private

Definition at line 113 of file RNA_TorsionMover.hh.

core::scoring::rna::RNA_FittedTorsionInfo protocols::swa::monte_carlo::RNA_TorsionMover::rna_fitted_torsion_info_

private

Definition at line 114 of file RNA_TorsionMover.hh.

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

src/protocols/swa/monte_carlo/RNA_TorsionMover.hh
src/protocols/swa/monte_carlo/RNA_TorsionMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation