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protocols::moves::TrialMover Class Reference

A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object. More...

#include <TrialMover.hh>

Inheritance diagram for protocols::moves::TrialMover:
Inheritance graph
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Public Types

typedef core::Real Real
 
- 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
 

Public Member Functions

 TrialMover ()
 
 TrialMover (MoverOP mover_in, MonteCarloOP mc_in)
 Constructs a TrialMover trialmover = TrialMover( mover_in , mc_in ) More...
 
 TrialMover (TrialMover const &object_to_copy)
 Copy constructor. More...
 
 ~TrialMover () override
 
virtual void initialize_weights (Real const start_weight, Real const end_weight, core::scoring::ScoreType score_type, int const ramp_cycles)
 
void apply (core::pose::Pose &pose) override
 Performs a single trial, apply the Mover and accept or reject the move based on the MonteCarlo acceptance criteria. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
Real acceptance_rate () const
 
int num_accepts () const
 Returns the number of moves accepted by this TrialMover. More...
 
void set_mc (MonteCarloOP mc_in)
 Sets the MonteCarlo object to <mc_in> More...
 
MoverOP mover () const
 Returns the underlying Mover. More...
 
MonteCarlo const & mc () const
 Returns the underlying MonteCarlo object. More...
 
StatsType keep_stats_type () const
 
void keep_stats_type (StatsType setting)
 
void set_input_pose (PoseCOP pose) override
 setter for poses contained for rms More...
 
void set_native_pose (PoseCOP pose) override
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 Requires that a MonteCarlo object has already been loaded into the basic::datacache::DataMap in a prior MONTECARLOS objects section. 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 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...
 
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...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
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 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...
 

Protected Attributes

MoverOP mover_
 
MonteCarloOP mc_
 
MoverStatistics stats_
 

Private Attributes

Real start_weight_
 
Real original_weight
 
Real ramp_weight
 
Real delta
 
StatsType stats_type_
 

Friends

std::ostream & operator<< (std::ostream &os, TrialMover const &mover)
 

Additional Inherited Members

- 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::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...
 

Detailed Description

A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object.

Common Methods: TrialMover.apply TrialMover.set_mc

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::moves::TrialMover::TrialMover ( )
protocols::moves::TrialMover::TrialMover ( MoverOP  mover_in,
MonteCarloOP  mc_in 
)

Constructs a TrialMover trialmover = TrialMover( mover_in , mc_in )

Mover mover_in /object defining what move to make MonteCarlo mc_in /object defining acceptance

References mc_, and mover_.

protocols::moves::TrialMover::TrialMover ( TrialMover const &  object_to_copy)

Copy constructor.

protocols::moves::TrialMover::~TrialMover ( )
overridedefault

Member Function Documentation

Real protocols::moves::TrialMover::acceptance_rate ( ) const
void protocols::moves::TrialMover::apply ( core::pose::Pose pose)
overridevirtual

Performs a single trial, apply the Mover and accept or reject the move based on the MonteCarlo acceptance criteria.

: the apply function for a trial

example(s): trialmover.apply(pose) See Also: Pose MonteCarlo MonteCarlo.boltzmann RepeatMover SequenceMover TrialMover

: the trial object is created with an mc object the mover is applied before doing an mc.boltzmann

Author
: Monica Berrondo

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_filters::EvaluatedTrialMover.

References protocols::moves::accept_reject, protocols::moves::MoverStatistics::accepted(), protocols::moves::MoverStatistics::add_score(), protocols::moves::all_stats, core::pose::Pose::energies(), keep_stats_type(), mc_, mover_, protocols::moves::no_stats, protocols::moves::MoverStatistics::print(), stats_, stats_type_, core::scoring::Energies::total_energy(), and core::scoring::total_score.

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::do_frag_cycles().

protocols::moves::MoverOP protocols::moves::TrialMover::clone ( ) const
overridevirtual

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.

protocols::moves::MoverOP protocols::moves::TrialMover::fresh_instance ( ) const
overridevirtual

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.

std::string protocols::moves::TrialMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_filters::EvaluatedTrialMover.

Referenced by protocols::moves::operator<<().

void protocols::moves::TrialMover::initialize_weights ( Real const  start_weight,
Real const  end_weight,
core::scoring::ScoreType  score_type,
int const  ramp_cycles 
)
virtual
StatsType protocols::moves::TrialMover::keep_stats_type ( ) const
inline
void protocols::moves::TrialMover::keep_stats_type ( StatsType  setting)
inline

References stats_type_.

MonteCarlo const& protocols::moves::TrialMover::mc ( ) const
inline

Returns the underlying MonteCarlo object.

References mc_.

MoverOP protocols::moves::TrialMover::mover ( ) const
inline

Returns the underlying Mover.

References mover_.

Referenced by protocols::moves::operator<<().

int protocols::moves::TrialMover::num_accepts ( ) const

Returns the number of moves accepted by this TrialMover.

References protocols::moves::MoverStatistics::num_accepted(), and stats_.

Referenced by protocols::moves::operator<<().

void protocols::moves::TrialMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Requires that a MonteCarlo object has already been loaded into the basic::datacache::DataMap in a prior MONTECARLOS objects section.

Reimplemented from protocols::moves::Mover.

References protocols::moves::accept_reject, protocols::moves::all_stats, mc_, mover_, protocols::moves::no_stats, protocols::rosetta_scripts::parse_mover_or_null(), and stats_type_.

void protocols::moves::TrialMover::set_input_pose ( PoseCOP  pose)
overridevirtual

setter for poses contained for rms

Reimplemented from protocols::moves::Mover.

References mover_, and protocols::moves::Mover::set_input_pose().

void protocols::moves::TrialMover::set_mc ( MonteCarloOP  mc_in)

Sets the MonteCarlo object to <mc_in>

example(s): trialmover.set_mc(mc) See Also: MonteCarlo MonteCarlo.boltzmann TrialMover

References mc_.

void protocols::moves::TrialMover::set_native_pose ( PoseCOP  pose)
overridevirtual

setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe

Reimplemented from protocols::moves::Mover.

References mover_, and protocols::moves::Mover::set_native_pose().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
TrialMover const &  mover 
)
friend

Member Data Documentation

Real protocols::moves::TrialMover::delta
private

Referenced by initialize_weights().

MonteCarloOP protocols::moves::TrialMover::mc_
protected
MoverOP protocols::moves::TrialMover::mover_
protected
Real protocols::moves::TrialMover::original_weight
private

Referenced by initialize_weights().

Real protocols::moves::TrialMover::ramp_weight
private

Referenced by initialize_weights().

Real protocols::moves::TrialMover::start_weight_
private

Referenced by initialize_weights().

MoverStatistics protocols::moves::TrialMover::stats_
protected
StatsType protocols::moves::TrialMover::stats_type_
private

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