#include <SymShakeStructureMover.hh>

Inheritance diagram for protocols::simple_moves::symmetry::SymShakeStructureMover:

Collaboration diagram for protocols::simple_moves::symmetry::SymShakeStructureMover:

Public Member Functions
	SymShakeStructureMover ()

	SymShakeStructureMover (core::scoring::ScoreFunctionOP s)

	SymShakeStructureMover (core::scoring::ScoreFunctionOP s, core::Real temperature)

	SymShakeStructureMover (core::scoring::ScoreFunctionOP s, core::Real ens_diversity, core::Real ens_div_tolerance)

virtual	~SymShakeStructureMover ()

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

core::scoring::symmetry::SymmetricScoreFunction	reduce_fa_rep (float fraction_fa_rep, core::scoring::ScoreFunction &s)

void	minimize_with_constraints (core::pose::Pose &p, core::scoring::ScoreFunction &s)

void	setup_for_run (core::pose::Pose &p)

void	run_mc (core::pose::Pose &p, core::scoring::ScoreFunction &s, core::Real temperature)

Public Member Functions inherited from protocols::simple_moves::ShakeStructureMover
	ShakeStructureMover ()

	ShakeStructureMover (core::scoring::ScoreFunctionOP s)

	ShakeStructureMover (core::scoring::ScoreFunctionOP s, core::Real temperature)

	ShakeStructureMover (core::scoring::ScoreFunctionOP s, core::Real ens_diversity, core::Real ens_div_tolerance)

virtual	~ShakeStructureMover ()

void	set_skip_low_temp_phase (bool truefalse)

void	set_mc_temperature (core::Real temp)

void	set_nrounds (int new_nrounds)

void	set_ramp_fa_rep (bool truefalse)

void	set_minimize_with_cst (bool truefalse)

void	set_scorefunction (core::scoring::ScoreFunction &s)

void	set_ensemble_diversity (core::Real ca_rmsd)

void	set_rmsd_target_tolerance (core::Real tol)

void	set_sc_min (bool truefalse)

core::Real	get_mc_temperature ()

bool	get_ramp_fa_rep ()

bool	get_minimize_with_cst ()

core::scoring::ScoreFunctionOP	get_scorefunction ()

core::Real	get_ensemble_diversity ()

core::Real	get_rmsd_target_tolerance ()

bool	get_sc_min ()

core::Real	get_harmonic_ca_cst_std_dev ()

core::Real	get_ensemble_ca_rmsd ()

bool	get_skip_low_temp_phase ()

bool	get_min_cst ()

bool	get_testing_phase ()

bool	get_scorefunction_initialized ()

core::scoring::ScoreFunctionOP	get_min_scorefunction ()

core::Size	get_nrounds ()

void	apply (core::pose::Pose &p)

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

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::simple_moves::ShakeStructureMover
void	set_testing_phase (bool truefalse)

void	set_mc_temp (core::Real temperature)

void	set_is_properly_initialized (bool truefalse)

void	set_min_scorefunction (core::scoring::ScoreFunctionOP scfxn)

core::scoring::ScoreFunction	reduce_fa_rep (float fraction_fa_rep, core::scoring::ScoreFunction &s)

virtual void	setup_ca_constraints (core::pose::Pose &pose, core::scoring::ScoreFunction &s, float const CA_cutoff, float const cst_tol)

core::Real	set_temp_based_on_ens_diversity (core::pose::Pose &p, core::scoring::ScoreFunction &s)

void	setup_movers (protocols::simple_moves::SmallMoverOP gsmall, protocols::simple_moves::ShearMoverOP gshear, core::Real small_H_angle_max, core::Real small_E_angle_max, core::Real small_L_angle_max, core::Real shear_H_angle_max, core::Real shear_E_angle_max, core::Real shear_L_angle_max)

void	create_ensemble (core::pose::Pose &p, core::scoring::ScoreFunction &s)

Detailed Description

Definition at line 44 of file SymShakeStructureMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::symmetry::SymShakeStructureMover::SymShakeStructureMover ( )

Definition at line 132 of file SymShakeStructureMover.cc.

protocols::simple_moves::symmetry::SymShakeStructureMover::SymShakeStructureMover ( core::scoring::ScoreFunctionOP s)

Definition at line 136 of file SymShakeStructureMover.cc.

protocols::simple_moves::symmetry::SymShakeStructureMover::SymShakeStructureMover	(	core::scoring::ScoreFunctionOP	s,
		core::Real	temperature
	)

Definition at line 140 of file SymShakeStructureMover.cc.

protocols::simple_moves::symmetry::SymShakeStructureMover::SymShakeStructureMover	(	core::scoring::ScoreFunctionOP	s,
		core::Real	ens_diversity,
		core::Real	ens_div_tolerance
	)

Definition at line 145 of file SymShakeStructureMover.cc.

protocols::simple_moves::symmetry::SymShakeStructureMover::~SymShakeStructureMover ( )

virtual

Definition at line 150 of file SymShakeStructureMover.cc.

Member Function Documentation

std::string protocols::simple_moves::symmetry::SymShakeStructureMover::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::ShakeStructureMover.

Definition at line 159 of file SymShakeStructureMover.cc.

void protocols::simple_moves::symmetry::SymShakeStructureMover::minimize_with_constraints	(	core::pose::Pose &	p,
		core::scoring::ScoreFunction &	s
	)

virtual

Reimplemented from protocols::simple_moves::ShakeStructureMover.

Definition at line 204 of file SymShakeStructureMover.cc.

References protocols::simple_moves::ShakeStructureMover::get_ramp_fa_rep(), protocols::simple_moves::ShakeStructureMover::get_sc_min(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::nblist_auto_update(), reduce_fa_rep(), and core::optimization::symmetry::SymAtomTreeMinimizer::run().

Referenced by run_mc().

core::scoring::symmetry::SymmetricScoreFunction protocols::simple_moves::symmetry::SymShakeStructureMover::reduce_fa_rep	(	float	fraction_fa_rep,
		core::scoring::ScoreFunction &	s
	)