#include <RNA_O2PrimeMover.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover:

Public Member Functions
	RNA_O2PrimeMover (core::scoring::ScoreFunctionOP scorefxn, bool const sample_all_o2prime, core::Real const sample_range_small, core::Real const sample_range_large)

	~RNA_O2PrimeMover () override

void	apply (core::pose::Pose &pose_to_visualize) override
	Main Method. More...

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

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

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, 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...

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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Private Member Functions
void	sample_near_o2prime_torsion (core::pose::Pose &pose, Size const moving_res, core::Real const sample_range)

Size	get_random_o2prime_residue (core::pose::Pose &pose)

Size	get_random_o2prime_residue_near_moving_residue (core::pose::Pose &pose, utility::vector1< Size > const &moving_res_list)

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_

bool const	sample_all_o2prime_

core::Real const	sample_range_small_

core::Real const	sample_range_large_

Additional Inherited Members
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::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::monte_carlo::rna::RNA_O2PrimeMover::RNA_O2PrimeMover	(	core::scoring::ScoreFunctionOP	scorefxn,
		bool const	sample_all_o2prime,
		core::Real const	sample_range_small,
		core::Real const	sample_range_large
	)

protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::~RNA_O2PrimeMover ( )

overridedefault

Member Function Documentation

void protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

void protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::apply	(	core::pose::Pose &	pose,
		std::string &	move_type
	)

References core::pose::full_model_info::get_moving_res_from_full_model_info(), get_random_o2prime_residue(), get_random_o2prime_residue_near_moving_residue(), core::scoring::rg, sample_all_o2prime_, sample_near_o2prime_torsion(), sample_range_large_, and sample_range_small_.

std::string protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

Size protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::get_random_o2prime_residue ( core::pose::Pose & pose )

private

References core::scoring::rg, and core::pose::Pose::size().

Referenced by apply().

Size protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::get_random_o2prime_residue_near_moving_residue	(	core::pose::Pose &	pose,
		utility::vector1< Size > const &	moving_res_list
	)

private

References core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by apply().

void protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::sample_near_o2prime_torsion	(	core::pose::Pose &	pose,
		Size const	moving_res,
		core::Real const	sample_range
	)

private

References core::chemical::rna::CHI, core::scoring::rg, core::pose::Pose::set_torsion(), and core::pose::Pose::torsion().

Referenced by apply().

Member Data Documentation

bool const protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::sample_all_o2prime_

private

Referenced by apply().

core::Real const protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::sample_range_large_

private

Referenced by apply().

core::Real const protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::sample_range_small_

private

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::scorefxn_

private

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

src/protocols/stepwise/monte_carlo/rna/RNA_O2PrimeMover.hh
src/protocols/stepwise/monte_carlo/rna/RNA_O2PrimeMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation