#include <ShearMinCCDTrial.hh>

Inheritance diagram for protocols::loops::loop_mover::refine::ShearMinCCDTrial:

Collaboration diagram for protocols::loops::loop_mover::refine::ShearMinCCDTrial:

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

virtual moves::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...

virtual void	show (std::ostream &out=std::cout)

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

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 (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...

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

Detailed Description

Definition at line 47 of file ShearMinCCDTrial.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 62 of file ShearMinCCDTrial.cc.

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 ///

Definition at line 118 of file ShearMinCCDTrial.cc.

References init().

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

copy constructor

Definition at line 69 of file ShearMinCCDTrial.cc.

References init_for_equal_operator_and_copy_constructor().

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

Definition at line 85 of file ShearMinCCDTrial.cc.

Member Function Documentation

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

virtual

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

Definition at line 128 of file ShearMinCCDTrial.cc.

References protocols::loops::Loops::add_loop(), protocols::loops::add_loop_flank_residues_bb_to_movemap(), protocols::simple_moves::BackboneMover::apply(), protocols::loops::ccd_close_loops(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc(), min_options_, minimizer(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::movemap(), nmoves_, core::pack::rotamer_trials(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn(), setup_objects(), and protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory().

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

virtual

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

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.

Definition at line 93 of file ShearMinCCDTrial.cc.

References ShearMinCCDTrial().

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

virtual

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).

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.

Definition at line 98 of file ShearMinCCDTrial.cc.

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.

Definition at line 88 of file ShearMinCCDTrial.cc.

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

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

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

private

Definition at line 168 of file ShearMinCCDTrial.cc.

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
	)