#include <RNA_SWA_MonteCarloMover.hh>

Inheritance diagram for protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover:

Collaboration diagram for protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover:

Public Member Functions
	RNA_SWA_MonteCarloMover (RNA_AddOrDeleteMoverOP rna_add_or_delete_mover, RNA_TorsionMoverOP rna_torsion_mover, RNA_O2StarMoverOP rna_o2star_mover, core::scoring::ScoreFunctionOP scorefxn)

	~RNA_SWA_MonteCarloMover ()

virtual void	apply (core::pose::Pose &pose_to_visualize)
	Apply the minimizer to one pose. More...

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

void	set_kT (core::Real const &setting)

void	set_sample_range_small (core::Real const setting)

void	set_sample_range_large (core::Real const setting)

void	set_num_cycles (Size const setting)

void	set_output_period (Size const setting)

void	set_do_add_delete (bool const setting)

void	set_silent_file (std::string const setting)

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	initialize_next_suite_atoms ()

void	output_silent_file (core::pose::Pose &pose, Size const count)

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 38 of file RNA_SWA_MonteCarloMover.hh.

Constructor & Destructor Documentation

protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::RNA_SWA_MonteCarloMover	(	RNA_AddOrDeleteMoverOP	rna_add_or_delete_mover,
		RNA_TorsionMoverOP	rna_torsion_mover,
		RNA_O2StarMoverOP	rna_o2star_mover,
		core::scoring::ScoreFunctionOP	scorefxn
	)

Definition at line 65 of file RNA_SWA_MonteCarloMover.cc.

References initialize_next_suite_atoms().

protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::~RNA_SWA_MonteCarloMover ( )

Definition at line 87 of file RNA_SWA_MonteCarloMover.cc.

Member Function Documentation

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

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

Definition at line 92 of file RNA_SWA_MonteCarloMover.cc.

References do_add_delete_, kT_, protocols::swa::monte_carlo::SubToFullInfo::moving_res_list(), protocols::swa::monte_carlo::nonconst_sub_to_full_info_from_pose(), num_cycles_, output_period_, output_silent_file(), protocols::RG(), rna_add_or_delete_mover_, rna_o2star_mover_, rna_torsion_mover_, sample_range_large_, sample_range_small_, and scorefxn_.

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 251 of file RNA_SWA_MonteCarloMover.cc.

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::initialize_next_suite_atoms ( )

private

Definition at line 146 of file RNA_SWA_MonteCarloMover.cc.

References next_suite_atoms_.

Referenced by RNA_SWA_MonteCarloMover().

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_silent_file	(	core::pose::Pose &	pose,
		Size const	count
	)

private

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::set_do_add_delete ( bool const setting)

inline

Definition at line 66 of file RNA_SWA_MonteCarloMover.hh.

References do_add_delete_.

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::set_kT ( core::Real const & setting)

inline

Definition at line 56 of file RNA_SWA_MonteCarloMover.hh.

References kT_.

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::set_num_cycles ( Size const setting)

inline

Definition at line 62 of file RNA_SWA_MonteCarloMover.hh.

References num_cycles_.

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::set_output_period ( Size const setting)

inline

Definition at line 64 of file RNA_SWA_MonteCarloMover.hh.

References output_period_.

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::set_sample_range_large ( core::Real const setting)

inline

Definition at line 60 of file RNA_SWA_MonteCarloMover.hh.

References sample_range_large_.

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::set_sample_range_small ( core::Real const setting)

inline

Definition at line 58 of file RNA_SWA_MonteCarloMover.hh.

References sample_range_small_.

void protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::set_silent_file ( std::string const setting)

inline

Definition at line 68 of file RNA_SWA_MonteCarloMover.hh.

References silent_file_.

Member Data Documentation

bool protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::do_add_delete_

private

Definition at line 89 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply(), and set_do_add_delete().

core::Real protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::kT_

private

Definition at line 87 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply(), and set_kT().

utility::vector1< std::string > protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::next_suite_atoms_

private

Definition at line 93 of file RNA_SWA_MonteCarloMover.hh.

Referenced by initialize_next_suite_atoms(), and output_silent_file().

Size protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::num_cycles_

private

Definition at line 86 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply(), and set_num_cycles().

Size protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_period_

private

Definition at line 86 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply(), and set_output_period().

RNA_AddOrDeleteMoverOP protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::rna_add_or_delete_mover_

private

Definition at line 80 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply().

RNA_O2StarMoverOP protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::rna_o2star_mover_

private

Definition at line 82 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply().

RNA_TorsionMoverOP protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::rna_torsion_mover_

private

Definition at line 81 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply().

core::Real protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::sample_range_large_

private

Definition at line 87 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply(), and set_sample_range_large().

core::Real protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::sample_range_small_

private

Definition at line 87 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply(), and set_sample_range_small().

core::scoring::ScoreFunctionOP protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::scorefxn_

private

Definition at line 84 of file RNA_SWA_MonteCarloMover.hh.

Referenced by apply().

std::string protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::silent_file_

private

Definition at line 90 of file RNA_SWA_MonteCarloMover.hh.

Referenced by output_silent_file(), and set_silent_file().

core::io::silent::SilentFileDataOP protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::silent_file_data_

private

Definition at line 91 of file RNA_SWA_MonteCarloMover.hh.

Referenced by output_silent_file().

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

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

Private Attributes
RNA_AddOrDeleteMoverOP	rna_add_or_delete_mover_

RNA_TorsionMoverOP	rna_torsion_mover_

RNA_O2StarMoverOP	rna_o2star_mover_

core::scoring::ScoreFunctionOP	scorefxn_

Size	num_cycles_

Size	output_period_

core::Real	sample_range_small_

core::Real	sample_range_large_

core::Real	kT_

bool	do_add_delete_

std::string	silent_file_

core::io::silent::SilentFileDataOP	silent_file_data_

utility::vector1< std::string >	next_suite_atoms_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation