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

#include <LoopRefineInnerCycleContainer.hh>

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

Public Member Functions

 LoopRefineInnerCycleContainer ()
 default constructor More...
 LoopRefineInnerCycleContainer (LoopRefineInnerCycleContainer const &rhs)
 copy constructor More...
LoopRefineInnerCycleContaineroperator= (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...
LoopRefineInnerCycleoperator= (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)
Moveroperator= (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 Stringsinfo ()
 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

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_


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 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

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 ( )

Member Function Documentation

void protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::add_inner_cycle_step ( LoopRefineInnerCycleOP  inner_cycle_step)
void protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::apply ( Pose pose)
protocols::moves::MoverOP protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::clone ( ) const

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

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

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

Referenced by init().

LoopRefineInnerCycleContainer & protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::operator= ( LoopRefineInnerCycleContainer const &  rhs)
void protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::register_options ( )

Associates relevant options with the LoopRefineInnerCycleContainer class.

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

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

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)
void protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_task_factory ( core::pack::task::TaskFactoryOP  tf)
void protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::setup_objects ( Pose const &  pose)
void protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::show ( std::ostream &  out = std::cout)

Friends And Related Function Documentation

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

Member Data Documentation

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

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