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protocols::loops::loop_mover::refine::SmallMinCCDTrial Class Reference

#include <SmallMinCCDTrial.hh>

Inheritance diagram for protocols::loops::loop_mover::refine::SmallMinCCDTrial:
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Collaboration diagram for protocols::loops::loop_mover::refine::SmallMinCCDTrial:
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Public Member Functions

 SmallMinCCDTrial ()
 default constructor More...
 
 SmallMinCCDTrial (SmallMinCCDTrial const &rhs)
 copy constructor More...
 
SmallMinCCDTrialoperator= (SmallMinCCDTrial const &rhs)
 assignment operator More...
 
virtual ~SmallMinCCDTrial ()
 
 SmallMinCCDTrial (LoopMover_Refine_CCDAP loop_mover, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf)
 
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)
 
core::Size number_of_moves () const
 
void set_number_of_moves (core::Size nmoves)
 
core::optimization::MinimizerOptionsOP minimizer_options () const
 
void set_minimizer_options (core::optimization::MinimizerOptionsOP minimizer_options)
 
- 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
 
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)
 
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...
 
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 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 LoopRefineInnerCycle 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 Member Functions

void setup_objects (Pose const &pose)
 
void init ()
 
void init_for_equal_operator_and_copy_constructor (SmallMinCCDTrial &lhs, SmallMinCCDTrial const &rhs)
 
void init_options ()
 
core::optimization::AtomTreeMinimizerOP minimizer (core::pose::Pose const &pose) const
 
void debug_zero (Pose &pose)
 
void debug_one (Pose &pose)
 
void debug_two (Pose &pose)
 
void debug_three (Pose &pose)
 
void debug_four (Pose &pose)
 
void debug_five (Pose &pose)
 

Private Attributes

core::Size nmoves_
 
core::optimization::MinimizerOptionsOP minimizer_options_
 
core::optimization::AtomTreeMinimizerOP minimizer_
 

Friends

std::ostream & operator<< (std::ostream &out, SmallMinCCDTrial const &small_min_ccd_trial)
 

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)
 

Constructor & Destructor Documentation

protocols::loops::loop_mover::refine::SmallMinCCDTrial::SmallMinCCDTrial ( )

default constructor

References init().

Referenced by clone(), and fresh_instance().

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

copy constructor

References init_for_equal_operator_and_copy_constructor().

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

References init().

Member Function Documentation

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply ( Pose pose)
virtual
protocols::moves::MoverOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::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 SmallMinCCDTrial().

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_five ( Pose pose)
private
void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_four ( Pose pose)
private
void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_one ( Pose pose)
private
void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_three ( Pose pose)
private
void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_two ( Pose pose)
private
void protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_zero ( Pose pose)
private
protocols::moves::MoverOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::fresh_instance ( ) const
virtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

References SmallMinCCDTrial().

std::string protocols::loops::loop_mover::refine::SmallMinCCDTrial::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::SmallMinCCDTrial::init ( void  )
private
void protocols::loops::loop_mover::refine::SmallMinCCDTrial::init_for_equal_operator_and_copy_constructor ( SmallMinCCDTrial lhs,
SmallMinCCDTrial const &  rhs 
)
private

References minimizer_.

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

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::init_options ( )
private

Referenced by init().

core::optimization::AtomTreeMinimizerOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer ( core::pose::Pose const &  pose) const
private

References core::pose::symmetry::is_symmetric(), and minimizer_.

Referenced by apply().

core::optimization::MinimizerOptionsOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer_options ( ) const

References minimizer_options_.

Referenced by set_minimizer_options().

core::Size protocols::loops::loop_mover::refine::SmallMinCCDTrial::number_of_moves ( ) const

References nmoves_.

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

Associates relevant options with the LoopRefineInnerCycle class.

bool protocols::loops::loop_mover::refine::SmallMinCCDTrial::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::SmallMinCCDTrial::set_minimizer_options ( core::optimization::MinimizerOptionsOP  minimizer_options)
void protocols::loops::loop_mover::refine::SmallMinCCDTrial::set_number_of_moves ( core::Size  nmoves)

References nmoves_.

void protocols::loops::loop_mover::refine::SmallMinCCDTrial::setup_objects ( Pose const &  pose)
private
void protocols::loops::loop_mover::refine::SmallMinCCDTrial::show ( std::ostream &  out = std::cout)
virtual

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
SmallMinCCDTrial const &  small_min_ccd_trial 
)
friend

Member Data Documentation

core::optimization::AtomTreeMinimizerOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer_
mutableprivate
core::optimization::MinimizerOptionsOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer_options_
private
core::Size protocols::loops::loop_mover::refine::SmallMinCCDTrial::nmoves_
private

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