#include <ShearMinCCDTrial.hh>

Public Member Functions
	ShearMinCCDTrial ()
	default constructor More...

	ShearMinCCDTrial (LoopMover_Refine_CCDAP loop_mover, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf)
	PUT THE LIST OF OPTIONS THAT ARE USED HERE ///. More...

	ShearMinCCDTrial (ShearMinCCDTrial const &rhs)
	copy constructor More...

ShearMinCCDTrial &	operator= (ShearMinCCDTrial const &rhs)
	assignment operator More...

	~ShearMinCCDTrial ()

virtual void	apply (Pose &pose)

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

virtual bool	reinitialize_for_new_input () const
	This mover retains state such that a fresh version is needed if the input Pose is about to change. More...

virtual moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

virtual void	show (std::ostream &out=std::cout) const
	Outputs details about the Mover, including current settings. More...

Public Member Functions inherited from protocols::loops::loop_mover::refine::LoopRefineInnerCycle
	LoopRefineInnerCycle ()
	default constructor More...

	LoopRefineInnerCycle (LoopRefineInnerCycle const &rhs)
	copy constructor More...

LoopRefineInnerCycle &	operator= (LoopRefineInnerCycle const &rhs)
	assignment operator More...

virtual	~LoopRefineInnerCycle ()

	LoopRefineInnerCycle (LoopMover_Refine_CCDAP loop_mover, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf)

bool	debug () const

void	set_debug (bool debug)

moves::MonteCarloOP	mc () const

virtual void	set_mc (moves::MonteCarloOP mc)

core::scoring::ScoreFunctionOP	scorefxn () const

virtual void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)

core::pack::task::TaskFactoryOP	task_factory () const

virtual void	set_task_factory (core::pack::task::TaskFactoryOP tf)

LoopMover_Refine_CCDAP	loop_mover () const

virtual void	set_loop_mover (LoopMover_Refine_CCDAP new_owner_in_town)

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

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...

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	setup_objects (Pose const &pose)

void	init ()

void	init_for_equal_operator_and_copy_constructor (ShearMinCCDTrial &lhs, ShearMinCCDTrial const &rhs)

void	init_options ()

core::optimization::AtomTreeMinimizerOP	minimizer (core::pose::Pose const &pose) const

Private Attributes
Size	nmoves_

core::optimization::MinimizerOptionsOP	min_options_

core::optimization::AtomTreeMinimizerOP	minimizer_

Friends
std::ostream &	operator<< (std::ostream &out, ShearMinCCDTrial const &loop_refine_shear_CCD_min_trial_inner_cycle)

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::loops::loop_mover::refine::LoopRefineInnerCycle
static void	register_options ()
	Associates relevant options with the LoopRefineInnerCycle class. More...

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::loops::loop_mover::refine::LoopRefineInnerCycle
core::kinematics::MoveMapOP	movemap () const

void	set_movemap (core::kinematics::MoveMapOP movemap)

Loops	get_one_random_loop () const

void	setup_objects (Pose const &pose)

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::loops::loop_mover::refine::ShearMinCCDTrial::ShearMinCCDTrial ( )

default constructor

References init().

Referenced by clone(), and fresh_instance().

protocols::loops::loop_mover::refine::ShearMinCCDTrial::ShearMinCCDTrial	(	LoopMover_Refine_CCDAP	loop_mover,
		moves::MonteCarloOP	mc,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::pack::task::TaskFactoryOP	tf
	)

PUT THE LIST OF OPTIONS THAT ARE USED HERE ///.

RECURSIVELY CALL REGISTER OPTIONS ON ALL MOVERS THAT THIS CLASS HAS AN OWNING_PTR TO ///

References init().

protocols::loops::loop_mover::refine::ShearMinCCDTrial::ShearMinCCDTrial ( ShearMinCCDTrial const & rhs )

copy constructor

References init_for_equal_operator_and_copy_constructor().

protocols::loops::loop_mover::refine::ShearMinCCDTrial::~ShearMinCCDTrial ( )

Member Function Documentation

void protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply ( Pose & pose )

virtual

Implements protocols::loops::loop_mover::refine::LoopRefineInnerCycle.

References protocols::loops::Loops::add_loop(), protocols::loops::add_loop_flank_residues_bb_to_movemap(), protocols::simple_moves::BackboneMover::apply(), protocols::moves::MonteCarlo::boltzmann(), protocols::loops::ccd_close_loops(), core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), loops, protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc(), min_options_, minimizer(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::movemap(), nmoves_, core::pack::task::PackerTask::repacking_residues(), core::pack::rotamer_trials(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), core::pack::task::PackerTask::set_bump_check(), setup_objects(), shear_moves, protocols::moves::MonteCarlo::show_scores(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory(), and temperature.

moves::MoverOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::clone ( ) const

virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References ShearMinCCDTrial().

moves::MoverOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::fresh_instance ( ) const

virtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References ShearMinCCDTrial().

std::string protocols::loops::loop_mover::refine::ShearMinCCDTrial::get_name ( ) const

virtual

Each derived class must specify its name.

Reimplemented from protocols::loops::loop_mover::refine::LoopRefineInnerCycle.

References protocols::moves::Mover::type().

Referenced by protocols::loops::loop_mover::refine::operator<<().

void protocols::loops::loop_mover::refine::ShearMinCCDTrial::init ( void )

private

References init_options(), min_options_, nmoves_, and protocols::moves::Mover::type().

Referenced by ShearMinCCDTrial().

void protocols::loops::loop_mover::refine::ShearMinCCDTrial::init_for_equal_operator_and_copy_constructor	(	ShearMinCCDTrial &	lhs,
		ShearMinCCDTrial const &	rhs
	)

private

References min_options_, and nmoves_.

Referenced by operator=(), and ShearMinCCDTrial().

void protocols::loops::loop_mover::refine::ShearMinCCDTrial::init_options ( )

private

Referenced by init().

core::optimization::AtomTreeMinimizerOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::minimizer ( core::pose::Pose const & pose ) const

private

References core::pose::symmetry::is_symmetric(), and minimizer_.

Referenced by apply().

ShearMinCCDTrial & protocols::loops::loop_mover::refine::ShearMinCCDTrial::operator= ( ShearMinCCDTrial const & rhs )

assignment operator

References init_for_equal_operator_and_copy_constructor(), and protocols::loops::loop_mover::refine::LoopRefineInnerCycle::operator=().

bool protocols::loops::loop_mover::refine::ShearMinCCDTrial::reinitialize_for_new_input ( ) const

virtual

This mover retains state such that a fresh version is needed if the input Pose is about to change.

Reimplemented from protocols::loops::loop_mover::refine::LoopRefineInnerCycle.

void protocols::loops::loop_mover::refine::ShearMinCCDTrial::setup_objects ( Pose const & pose )

private

References protocols::loops::loop_mover::refine::LoopRefineInnerCycle::setup_objects().

Referenced by apply().

void protocols::loops::loop_mover::refine::ShearMinCCDTrial::show ( std::ostream & output = std::cout ) const

virtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::loops::loop_mover::refine::LoopRefineInnerCycle.

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		ShearMinCCDTrial const &	loop_refine_shear_CCD_min_trial_inner_cycle
	)

friend

Member Data Documentation

core::optimization::MinimizerOptionsOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::min_options_

private

Referenced by apply(), init(), and init_for_equal_operator_and_copy_constructor().

core::optimization::AtomTreeMinimizerOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::minimizer_

mutableprivate

Referenced by minimizer().

Size protocols::loops::loop_mover::refine::ShearMinCCDTrial::nmoves_

private

Referenced by apply(), init(), and init_for_equal_operator_and_copy_constructor().

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

src/protocols/loops/loop_mover/refine/ShearMinCCDTrial.hh
src/protocols/loops/loop_mover/refine/ShearMinCCDTrial.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation