protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer Class Reference

#include <LoopRefineInnerCycleContainer.hh>

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

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

Public Member Functions
	LoopRefineInnerCycleContainer ()
	default constructor More...
	LoopRefineInnerCycleContainer (LoopRefineInnerCycleContainer const &rhs)
	copy constructor More...
LoopRefineInnerCycleContainer &	operator= (LoopRefineInnerCycleContainer const &rhs)
	assignment operator More...
virtual	~LoopRefineInnerCycleContainer ()
virtual void	apply (Pose &)
virtual std::string	get_name () const
	Each derived class must specify its name. More...
virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...
virtual protocols::moves::MoverOP	fresh_instance () const
	fresh_instance returns a default-constructed object for JD2 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)
void	add_inner_cycle_step (LoopRefineInnerCycleOP inner_cycle_step)
virtual void	set_mc (moves::MonteCarloOP mc)
virtual void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
virtual void	set_task_factory (core::pack::task::TaskFactoryOP tf)
virtual void	set_loop_mover (LoopMover_Refine_CCDAP new_owner_in_town)
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...
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
core::scoring::ScoreFunctionOP	scorefxn () const
core::pack::task::TaskFactoryOP	task_factory () const
LoopMover_Refine_CCDAP	loop_mover () const
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...
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

Static Public Member Functions
static void	register_options ()
	Associates relevant options with the LoopRefineInnerCycleContainer class. More...
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. 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...

Private Types
typedef utility::vector1 < LoopRefineInnerCycleOP >	InnerCycleList

Private Member Functions
void	setup_objects (Pose const &pose)
void	init ()
void	init_for_equal_operator_and_copy_constructor (LoopRefineInnerCycleContainer &lhs, LoopRefineInnerCycleContainer const &rhs)
void	init_options ()

Private Attributes
InnerCycleList	inner_cycle_list_
moves::SequenceMoverOP	inner_cycle_steps_

Friends
std::ostream &	operator<< (std::ostream &out, LoopRefineInnerCycleContainer const &loop_refine_inner_cycle_container)

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
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)

Member Typedef Documentation

typedef utility::vector1< LoopRefineInnerCycleOP > protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::InnerCycleList

private

Constructor & Destructor Documentation

protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::LoopRefineInnerCycleContainer

(

)

default constructor

References init().

Referenced by clone(), and fresh_instance().

protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::LoopRefineInnerCycleContainer

(

LoopRefineInnerCycleContainer const &

rhs)

copy constructor

References init_for_equal_operator_and_copy_constructor().

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

virtual

Member Function Documentation

void protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::add_inner_cycle_step

(

LoopRefineInnerCycleOP

inner_cycle_step)

References inner_cycle_list_, and inner_cycle_steps_.

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

virtual

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

References inner_cycle_steps_, and setup_objects().

protocols::moves::MoverOP protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::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.

References LoopRefineInnerCycleContainer().

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

virtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

References LoopRefineInnerCycleContainer().

std::string protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::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::LoopRefineInnerCycleContainer::init ( void  )

private

References init_options(), inner_cycle_list_, inner_cycle_steps_, and protocols::moves::Mover::type().

Referenced by LoopRefineInnerCycleContainer().

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

private

References inner_cycle_list_, and inner_cycle_steps_.

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

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

private

Referenced by init().

LoopRefineInnerCycleContainer & protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::operator=

(

LoopRefineInnerCycleContainer const &

rhs)

assignment operator

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

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

static

Associates relevant options with the LoopRefineInnerCycleContainer class.

bool protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::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::LoopRefineInnerCycleContainer::set_loop_mover ( LoopMover_Refine_CCDAP  new_owner_in_town)

virtual

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

References inner_cycle_list_, and protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_loop_mover().

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

virtual

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

References inner_cycle_list_, and protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_mc().

void protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_native_pose ( PoseCOP  pose)

virtual

setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe

Reimplemented from protocols::moves::Mover.

References inner_cycle_list_, and protocols::moves::Mover::set_native_pose().

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

virtual

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

References inner_cycle_list_, and protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_scorefxn().

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

virtual

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

References inner_cycle_list_, and protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_task_factory().

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

private

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

Referenced by apply().

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

virtual

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

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out, LoopRefineInnerCycleContainer const &  loop_refine_inner_cycle_container  )

friend

Member Data Documentation

InnerCycleList protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::inner_cycle_list_

private

Referenced by add_inner_cycle_step(), init(), init_for_equal_operator_and_copy_constructor(), protocols::loops::loop_mover::refine::operator<<(), set_loop_mover(), set_mc(), set_native_pose(), set_scorefxn(), and set_task_factory().

moves::SequenceMoverOP protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::inner_cycle_steps_

private

Referenced by add_inner_cycle_step(), 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/LoopRefineInnerCycleContainer.hh
• src/protocols/loops/loop_mover/refine/LoopRefineInnerCycleContainer.cc