Rosetta Protocols  2014.35
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protocols::loops::loop_mover::refine::ShearMinCCDTrial Class Reference

#include <ShearMinCCDTrial.hh>

Public Member Functions

 ShearMinCCDTrial ()
 default constructor More...
 
 ShearMinCCDTrial (LoopMover_Refine_CCDAP loop_mover, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf)
 PUT THE LIST OF OPTIONS THAT ARE USED HERE ///. More...
 
 ShearMinCCDTrial (ShearMinCCDTrial const &rhs)
 copy constructor More...
 
ShearMinCCDTrialoperator= (ShearMinCCDTrial const &rhs)
 assignment operator More...
 
 ~ShearMinCCDTrial ()
 
virtual void apply (Pose &pose)
 
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 moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual void show (std::ostream &out=std::cout) const
 Outputs details about the Mover, including current settings. 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
 
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
 
void set_type (std::string const &setting)
 
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 (TagCOP tag, basic::datacache::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
 Inform 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
 

Private Member Functions

void setup_objects (Pose const &pose)
 
void init ()
 
void init_for_equal_operator_and_copy_constructor (ShearMinCCDTrial &lhs, ShearMinCCDTrial const &rhs)
 
void init_options ()
 
core::optimization::AtomTreeMinimizerOP minimizer (core::pose::Pose const &pose) const
 

Private Attributes

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

Friends

std::ostream & operator<< (std::ostream &out, ShearMinCCDTrial const &loop_refine_shear_CCD_min_trial_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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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. More...
 
- 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)
 
- 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...
 

Constructor & Destructor Documentation

protocols::loops::loop_mover::refine::ShearMinCCDTrial::ShearMinCCDTrial ( )

default constructor

References init().

Referenced by clone(), and fresh_instance().

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

PUT THE LIST OF OPTIONS THAT ARE USED HERE ///.

RECURSIVELY CALL REGISTER OPTIONS ON ALL MOVERS THAT THIS CLASS HAS AN OWNING_PTR TO ///

References init().

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

copy constructor

References init_for_equal_operator_and_copy_constructor().

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

Member Function Documentation

void protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply ( Pose pose)
virtual
moves::MoverOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::clone ( ) const
virtual

Return a clone of the Mover object.

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 ShearMinCCDTrial().

moves::MoverOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::fresh_instance ( ) const
virtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References ShearMinCCDTrial().

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

References min_options_, and nmoves_.

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

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

Referenced by init().

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

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

Referenced by apply().

ShearMinCCDTrial & protocols::loops::loop_mover::refine::ShearMinCCDTrial::operator= ( ShearMinCCDTrial const &  rhs)
bool protocols::loops::loop_mover::refine::ShearMinCCDTrial::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::ShearMinCCDTrial::setup_objects ( Pose const &  pose)
private
void protocols::loops::loop_mover::refine::ShearMinCCDTrial::show ( std::ostream &  output = std::cout) const
virtual

Outputs details about the Mover, including current settings.

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

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

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
ShearMinCCDTrial const &  loop_refine_shear_CCD_min_trial_inner_cycle 
)
friend

Member Data Documentation

core::optimization::MinimizerOptionsOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::min_options_
private
core::optimization::AtomTreeMinimizerOP protocols::loops::loop_mover::refine::ShearMinCCDTrial::minimizer_
mutableprivate

Referenced by minimizer().

Size protocols::loops::loop_mover::refine::ShearMinCCDTrial::nmoves_
private

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