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

#include <SmallMinCCDTrial.hh>

Inheritance diagram for protocols::loops::loop_mover::refine::SmallMinCCDTrial:
Inheritance graph
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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...
 
 ~SmallMinCCDTrial () override
 
 SmallMinCCDTrial (LoopMover_Refine_CCDAP loop_mover, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::TaskFactoryOP tf)
 
void apply (Pose &) override
 Main Method. More...
 
protocols::moves::MoverOP clone () const override
 Each derived class must specify its name. More...
 
protocols::moves::MoverOP fresh_instance () const override
 fresh_instance returns a default-constructed object for JD2 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...
 
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)
 
std::string get_name () const override
 Each derived class must specify its name. 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...
 
 ~LoopRefineInnerCycle () override
 
 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 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 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...
 
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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void register_options ()
 Associates relevant options with the LoopRefineInnerCycle class. More...
 
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

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::TagCOP TagCOP
 
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)
 
- 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::SmallMinCCDTrial::SmallMinCCDTrial ( )

default constructor

References init().

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 ( )
overridedefault
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 )
overridevirtual
protocols::moves::MoverOP protocols::loops::loop_mover::refine::SmallMinCCDTrial::clone ( ) const
overridevirtual

Each derived class must specify its name.

Reimplemented from protocols::moves::Mover.

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
overridevirtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

std::string protocols::loops::loop_mover::refine::SmallMinCCDTrial::get_name ( ) const
overridevirtual

Each derived class must specify its name.

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

References mover_name().

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().

std::string protocols::loops::loop_mover::refine::SmallMinCCDTrial::mover_name ( )
static
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::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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
overridevirtual

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 &  output = std::cout) const
overridevirtual

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,
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: