#include <LoopRefineInnerCycle.hh>

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

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

Public Member Functions
	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)

virtual void	apply (Pose &)=0

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

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 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 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

Static Public Member Functions
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. 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
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...

Private Member Functions
void	init ()

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

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

void	init_options ()

Private Attributes
bool	debug_

LoopMover_Refine_CCDAP	loop_mover_that_owns_me_

moves::MonteCarloOP	mc_

core::scoring::ScoreFunctionOP	scorefxn_

core::pack::task::TaskFactoryOP	tf_

core::kinematics::MoveMapOP	movemap_

Friends
std::ostream &	operator<< (std::ostream &out, LoopRefineInnerCycle const &loop_refine_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

Constructor & Destructor Documentation

protocols::loops::loop_mover::refine::LoopRefineInnerCycle::LoopRefineInnerCycle ( )

default constructor

References init().

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

copy constructor

References init_for_equal_operator_and_copy_constructor().

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

virtual

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

References init().

Member Function Documentation

virtual void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::apply ( Pose & )

pure virtual

Implements protocols::moves::Mover.

Implemented in protocols::loops::loop_mover::refine::ShearMinCCDTrial, protocols::loops::loop_mover::refine::SmallMinCCDTrial, protocols::loops::loop_mover::refine::RepackTrial, and protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer.

bool protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug ( ) const

References debug_.

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_five(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_four(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_one(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_three(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_two(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_zero(), and set_debug().

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

virtual

Each derived class must specify its name.

Implements protocols::moves::Mover.

Reimplemented in protocols::loops::loop_mover::refine::ShearMinCCDTrial, protocols::loops::loop_mover::refine::SmallMinCCDTrial, protocols::loops::loop_mover::refine::RepackTrial, and protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer.

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

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

Loops protocols::loops::loop_mover::refine::LoopRefineInnerCycle::get_one_random_loop ( ) const

protected

References protocols::loops::Loops::add_loop(), and loop_mover().

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply().

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

private

Referenced by LoopRefineInnerCycle().

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

private

References init_options(), loop_mover(), loop_mover_that_owns_me_, mc(), mc_, scorefxn(), scorefxn_, tf_, and protocols::moves::Mover::type().

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

private

References debug_, loop_mover_that_owns_me_, mc_, movemap_, scorefxn_, and tf_.

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

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

private

References core::pack::interaction_graph::debug, and set_debug().

Referenced by init().

LoopMover_Refine_CCDAP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover ( ) const

References loop_mover_that_owns_me_.

moves::MonteCarloOP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc ( ) const

References mc_.

Referenced by protocols::loops::loop_mover::refine::RepackTrial::apply(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), init(), and set_mc().

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

protected

References movemap_.

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), and set_movemap().

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

assignment operator

References init_for_equal_operator_and_copy_constructor().

Referenced by protocols::loops::loop_mover::refine::RepackTrial::operator=(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::operator=(), protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::operator=(), and protocols::loops::loop_mover::refine::ShearMinCCDTrial::operator=().

void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::register_options ( )

static

Associates relevant options with the LoopRefineInnerCycle class.

bool protocols::loops::loop_mover::refine::LoopRefineInnerCycle::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::moves::Mover.

Reimplemented in protocols::loops::loop_mover::refine::ShearMinCCDTrial, protocols::loops::loop_mover::refine::SmallMinCCDTrial, protocols::loops::loop_mover::refine::RepackTrial, and protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer.

core::scoring::ScoreFunctionOP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn ( ) const

References scorefxn_.

void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_debug ( bool debug)

References debug(), and debug_.

Referenced by init_options().

void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_loop_mover ( LoopMover_Refine_CCDAP new_owner_in_town)

virtual

Reimplemented in protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer.

References loop_mover_that_owns_me_.

Referenced by protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_loop_mover().

void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_mc ( moves::MonteCarloOP mc)

virtual

Reimplemented in protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer.

References mc(), and mc_.

Referenced by protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_mc().

void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_movemap ( core::kinematics::MoveMapOP movemap)

protected

References movemap(), and movemap_.

void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_scorefxn ( core::scoring::ScoreFunctionOP scorefxn)

virtual

Reimplemented in protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer.

References scorefxn(), and scorefxn_.

Referenced by protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_scorefxn().

void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_task_factory ( core::pack::task::TaskFactoryOP tf)

virtual

Reimplemented in protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer.

References tf_.

Referenced by protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_task_factory().

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

protected

References get_name(), loop_mover_that_owns_me_, mc_, scorefxn_, tf_, and protocols::loops::loop_mover::refine::TR().

Referenced by protocols::loops::loop_mover::refine::RepackTrial::setup_objects(), protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::setup_objects(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::setup_objects(), and protocols::loops::loop_mover::refine::SmallMinCCDTrial::setup_objects().

void protocols::loops::loop_mover::refine::LoopRefineInnerCycle::show ( std::ostream & out = std::cout)

virtual

Reimplemented in protocols::loops::loop_mover::refine::ShearMinCCDTrial, protocols::loops::loop_mover::refine::SmallMinCCDTrial, protocols::loops::loop_mover::refine::RepackTrial, and protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer.

core::pack::task::TaskFactoryOP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory ( ) const

References tf_.

Referenced by protocols::loops::loop_mover::refine::RepackTrial::apply(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), and protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply().

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		LoopRefineInnerCycle const &	loop_refine_inner_cycle
	)

friend

Member Data Documentation

bool protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug_

private

Referenced by debug(), init_for_equal_operator_and_copy_constructor(), and set_debug().

LoopMover_Refine_CCDAP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover_that_owns_me_

private

Referenced by init(), init_for_equal_operator_and_copy_constructor(), loop_mover(), set_loop_mover(), and setup_objects().

moves::MonteCarloOP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc_

private

Referenced by init(), init_for_equal_operator_and_copy_constructor(), mc(), set_mc(), and setup_objects().

core::kinematics::MoveMapOP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::movemap_

mutableprivate

Referenced by init_for_equal_operator_and_copy_constructor(), movemap(), and set_movemap().

core::scoring::ScoreFunctionOP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn_

private

Referenced by init(), init_for_equal_operator_and_copy_constructor(), scorefxn(), set_scorefxn(), and setup_objects().

core::pack::task::TaskFactoryOP protocols::loops::loop_mover::refine::LoopRefineInnerCycle::tf_

private

Referenced by init(), init_for_equal_operator_and_copy_constructor(), set_task_factory(), setup_objects(), and task_factory().

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

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

Public Member Functions

Static Public Member Functions

Protected 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