Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
protocols::loops::loop_mover::refine::LoopRefineInnerCycle Class Referenceabstract

#include <LoopRefineInnerCycle.hh>

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

Public Member Functions

 LoopRefineInnerCycle ()
 default constructor More...
 LoopRefineInnerCycle (LoopRefineInnerCycle const &rhs)
 copy constructor More...
LoopRefineInnerCycleoperator= (LoopRefineInnerCycle const &rhs)
 assignment operator More...
 ~LoopRefineInnerCycle () override
 LoopRefineInnerCycle (LoopMover_Refine_CCDAP loop_mover, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf)
void apply (Pose &) override=0
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. More...
bool reinitialize_for_new_input () const override
 This mover retains state such that a fresh version is needed if the input Pose is about to change. More...
void show (std::ostream &out=std::cout) const override
 Outputs details about the Mover, including current settings. More...
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 MoverOP create ()
MoverCOP get_self_ptr () const
MoverOP get_self_ptr ()
MoverCAP get_self_weak_ptr () const
MoverAP get_self_weak_ptr ()
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
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...
virtual MoverOP clone () const
 Return a clone of the Mover object. 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...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
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...
void set_type (std::string const &setting)
 Set the 'type' string. More...
std::string get_type () const
void type (const std::string &type_in)
 Set the 'type' string. More...
std::string const & type () const
 Get the set 'type' string. More...
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void set_current_tag (std::string const &new_tag)
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...
virtual core::Real last_proposal_density_ratio ()
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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

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. 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_


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::TagCOP TagCOP
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings

Constructor & Destructor Documentation

◆ LoopRefineInnerCycle() [1/3]

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

default constructor

References init().

◆ LoopRefineInnerCycle() [2/3]

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

copy constructor

References init_for_equal_operator_and_copy_constructor().

◆ ~LoopRefineInnerCycle()

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

◆ LoopRefineInnerCycle() [3/3]

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(), loop_mover(), mc(), and scorefxn().

Member Function Documentation

◆ apply()

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

◆ debug()

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

◆ get_name()

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

◆ get_one_random_loop()

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

◆ init() [1/2]

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

Referenced by LoopRefineInnerCycle().

◆ init() [2/2]

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 

◆ init_for_equal_operator_and_copy_constructor()

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

◆ init_options()

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

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

Referenced by init().

◆ loop_mover()

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

◆ mc()

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

◆ movemap()

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

◆ operator=()

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

◆ register_options()

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

Associates relevant options with the LoopRefineInnerCycle class.

◆ reinitialize_for_new_input()

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

◆ scorefxn()

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

◆ set_debug()

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

References debug(), and debug_.

Referenced by init_options().

◆ set_loop_mover()

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

◆ set_mc()

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

◆ set_movemap()

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

References movemap(), and movemap_.

◆ set_scorefxn()

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

◆ set_task_factory()

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

◆ setup_objects()

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

◆ show()

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

Outputs details about the Mover, including current settings.

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

Reimplemented from protocols::moves::Mover.

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

References core::conformation::membrane::out.

◆ task_factory()

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

Friends And Related Function Documentation

◆ operator<<

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

Member Data Documentation

◆ debug_

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

◆ loop_mover_that_owns_me_

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

◆ mc_

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

◆ movemap_

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

◆ scorefxn_

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

◆ tf_

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

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