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protocols::simple_moves::rational_mc::RationalMonteCarlo Class Reference

#include <RationalMonteCarlo.hh>

Inheritance diagram for protocols::simple_moves::rational_mc::RationalMonteCarlo:
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Public Member Functions

 RationalMonteCarlo (moves::MoverOP mover, ScoreFunctionCOP score, core::Size num_trials, core::Real temperature, bool recover_low)
 
void apply (Pose &pose) override
 Applies the underlying mover to <pose> the specified number of times. More...
 
std::string get_name () const override
 Returns this mover's name. More...
 
bool recover_low () const
 
moves::MoverOP mover () const
 
core::Size num_trials () const
 
core::Real temperature () const
 
const
core::scoring::ScoreFunction
score_function () const
 
void reset (const core::pose::Pose &pose)
 Updates the last accepted and lowest scoring pose members of the MonteCarlo member variable to the score of the specified pose. More...
 
const core::pose::Poselowest_score_pose () const
 
const core::pose::Poselast_accepted_pose () const
 
void set_mover (moves::MoverOP mover)
 
void set_recover_low (bool recover_low)
 
void set_num_trials (core::Size num_trials)
 
void set_temperature (core::Real temperature)
 
void enable_autotemp (core::Real quench)
 
void disable_autotemp ()
 
void set_score_function (core::scoring::ScoreFunctionOP score)
 Updates the score function. Before calling this method, make sure that apply() has been called at least once on a non-empty pose. More...
 
core::Size add_trigger (const RationalMonteCarloTrigger &trigger)
 Registers the specified trigger with this instance. Returns a unique identifier for referring to this trigger in subsequent operations. More...
 
void remove_trigger (core::Size trigger_id)
 Unregisters the trigger with the given unique identifier. More...
 
- 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 bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). 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 void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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...
 

Protected Member Functions

void fire_all_triggers (const Pose &pose)
 Executes all triggers attached to this instance. The order of trigger execution is undefined. Do not assume, depend, or in any way rely upon a partiular ordering. More...
 
- 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 Types

typedef core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 

Private Attributes

moves::MoverOP mover_
 Underlying mover. More...
 
moves::MonteCarloOP mc_
 Determines whether applications of the base mover should be accepted by applying the Metropolis criterion to the pose. More...
 
core::Size num_trials_
 Number of times to execute the underlying mover in calls to apply() More...
 
bool recover_low_
 Determines whether the low scoring pose should be recovered at the conclusion of the apply() method. More...
 
Triggers triggers_
 Collection of function callbacks. More...
 
core::Size next_trigger_id_
 Next trigger id to be assigned. More...
 

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
 
- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::rational_mc::RationalMonteCarlo::RationalMonteCarlo ( moves::MoverOP  mover,
ScoreFunctionCOP  score,
core::Size  num_trials,
core::Real  temperature,
bool  recover_low 
)

Member Function Documentation

Size protocols::simple_moves::rational_mc::RationalMonteCarlo::add_trigger ( const RationalMonteCarloTrigger trigger)

Registers the specified trigger with this instance. Returns a unique identifier for referring to this trigger in subsequent operations.

References next_trigger_id_, and triggers_.

void protocols::simple_moves::rational_mc::RationalMonteCarlo::apply ( Pose pose)
overridevirtual

Applies the underlying mover to <pose> the specified number of times.

Implements protocols::moves::Mover.

References fire_all_triggers(), mc_, mover_, num_trials(), and recover_low().

Referenced by protocols::star::StarAbinitio::apply().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::disable_autotemp ( )

References mc_.

void protocols::simple_moves::rational_mc::RationalMonteCarlo::enable_autotemp ( core::Real  quench)

References mc_.

Referenced by protocols::star::StarAbinitio::apply().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::fire_all_triggers ( const Pose pose)
protected

Executes all triggers attached to this instance. The order of trigger execution is undefined. Do not assume, depend, or in any way rely upon a partiular ordering.

References protocols::hybridization::t, and triggers_.

Referenced by apply().

std::string protocols::simple_moves::rational_mc::RationalMonteCarlo::get_name ( ) const
overridevirtual

Returns this mover's name.

Implements protocols::moves::Mover.

const Pose & protocols::simple_moves::rational_mc::RationalMonteCarlo::last_accepted_pose ( ) const

References mc_.

const Pose & protocols::simple_moves::rational_mc::RationalMonteCarlo::lowest_score_pose ( ) const

References mc_.

MoverOP protocols::simple_moves::rational_mc::RationalMonteCarlo::mover ( ) const

References mover_.

Referenced by set_mover().

Size protocols::simple_moves::rational_mc::RationalMonteCarlo::num_trials ( ) const

References num_trials_.

Referenced by apply(), and set_num_trials().

bool protocols::simple_moves::rational_mc::RationalMonteCarlo::recover_low ( ) const

References recover_low_.

Referenced by apply(), and set_recover_low().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::remove_trigger ( core::Size  trigger_id)

Unregisters the trigger with the given unique identifier.

References triggers_.

void protocols::simple_moves::rational_mc::RationalMonteCarlo::reset ( const core::pose::Pose pose)

Updates the last accepted and lowest scoring pose members of the MonteCarlo member variable to the score of the specified pose.

References mc_.

const ScoreFunction & protocols::simple_moves::rational_mc::RationalMonteCarlo::score_function ( ) const

References mc_.

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_mover ( moves::MoverOP  mover)

References mover(), and mover_.

Referenced by protocols::star::configure_rmc().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_num_trials ( core::Size  num_trials)
void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_recover_low ( bool  recover_low)
void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_score_function ( core::scoring::ScoreFunctionOP  score)

Updates the score function. Before calling this method, make sure that apply() has been called at least once on a non-empty pose.

References mc_.

Referenced by protocols::star::configure_rmc().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_temperature ( core::Real  temperature)

References mc_.

Referenced by protocols::star::configure_rmc().

Real protocols::simple_moves::rational_mc::RationalMonteCarlo::temperature ( ) const

References mc_.

Referenced by RationalMonteCarlo().

Member Data Documentation

moves::MonteCarloOP protocols::simple_moves::rational_mc::RationalMonteCarlo::mc_
private

Determines whether applications of the base mover should be accepted by applying the Metropolis criterion to the pose.

Referenced by apply(), disable_autotemp(), enable_autotemp(), last_accepted_pose(), lowest_score_pose(), RationalMonteCarlo(), reset(), score_function(), set_score_function(), set_temperature(), and temperature().

moves::MoverOP protocols::simple_moves::rational_mc::RationalMonteCarlo::mover_
private

Underlying mover.

Referenced by apply(), mover(), and set_mover().

core::Size protocols::simple_moves::rational_mc::RationalMonteCarlo::next_trigger_id_
private

Next trigger id to be assigned.

Referenced by add_trigger().

core::Size protocols::simple_moves::rational_mc::RationalMonteCarlo::num_trials_
private

Number of times to execute the underlying mover in calls to apply()

Referenced by num_trials(), and set_num_trials().

bool protocols::simple_moves::rational_mc::RationalMonteCarlo::recover_low_
private

Determines whether the low scoring pose should be recovered at the conclusion of the apply() method.

Referenced by recover_low(), and set_recover_low().

Triggers protocols::simple_moves::rational_mc::RationalMonteCarlo::triggers_
private

Collection of function callbacks.

Referenced by add_trigger(), fire_all_triggers(), and remove_trigger().


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