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protocols::canonical_sampling::MetropolisHastingsMover Class Reference

#include <MetropolisHastingsMover.hh>

Inheritance diagram for protocols::canonical_sampling::MetropolisHastingsMover:
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Public Member Functions

 MetropolisHastingsMover ()
 
 MetropolisHastingsMover (MetropolisHastingsMover const &metropolis_hastings_mover)
 
virtual ~MetropolisHastingsMover ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). 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...
 
virtual bool reinitialize_for_new_input () const
 this function informs 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 void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
protocols::moves::MonteCarloCOP monte_carlo () const
 
void set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo)
 
void set_tempering (TemperatureControllerOP)
 
TemperatureControllerCOP tempering () const
 
core::Size ntrials () const
 
void set_ntrials (core::Size ntrials)
 
std::string const & output_name () const
 
void set_output_name (std::string const &output_name)
 
std::string output_file_name (std::string const &suffix, bool cumulate_jobs=false, bool cumulate_replicas=false) const
 
bool finished () const
 
virtual ThermodynamicMoverOP random_mover ()
 
virtual void add_mover (ThermodynamicMoverOP mover, core::Real weight, utility::tag::TagPtr const &subtag)
 
virtual void add_mover (ThermodynamicMoverOP mover, core::Real weight)
 
void add_backrub_mover (core::Real weight)
 
void add_small_mover (core::Real weight)
 
void add_shear_mover (core::Real weight)
 
void add_sidechain_mover (core::Real weight, core::Real prob_uniform, core::Real prob_withinrot, bool preserve_cbeta)
 
void add_sidechain_mc_mover (core::Real weight, core::Real prob_uniform, core::Real prob_withinrot, bool preserve_cbeta, core::Size ntrials)
 
void add_observer (ThermodynamicObserverOP observer)
 
ThermodynamicMover const & last_move () const
 
bool last_accepted () const
 
- 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)
 
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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Protected Types

typedef utility::vector1
< ThermodynamicObserverOP
ObserverList
 

Protected Member Functions

TemperatureControllerOP const & tempering ()
 
ThermodynamicMoverOP mover_by_index (numeric::Size idx) const
 
void wind_down_simulation (core::pose::Pose &pose)
 
core::Size prepare_simulation (core::pose::Pose &pose)
 
void set_last_accepted (bool setting)
 
void set_last_move (ThermodynamicMoverOP setting)
 
ObserverList const & observers ()
 
protocols::moves::MonteCarlononconst_monte_carlo ()
 
- 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 Attributes

protocols::moves::MonteCarloOP monte_carlo_
 configurables... More...
 
core::Size ntrials_
 
std::string output_name_
 
utility::vector1
< ThermodynamicMoverOP
movers_
 
utility::vector1
< ThermodynamicObserverOP
observers_
 
TemperatureControllerOP tempering_
 
numeric::random::WeightedSampler weighted_sampler_
 
ThermodynamicMoverOP last_move_
 some status is necessary for the observers More...
 
bool last_accepted_
 
core::Size trial_
 
bool output_name_from_job_distributor_
 

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
 
- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::canonical_sampling::MetropolisHastingsMover::MetropolisHastingsMover ( )

Referenced by fresh_instance().

protocols::canonical_sampling::MetropolisHastingsMover::MetropolisHastingsMover ( MetropolisHastingsMover const &  metropolis_hastings_mover)
protocols::canonical_sampling::MetropolisHastingsMover::~MetropolisHastingsMover ( )
virtual

Member Function Documentation

void protocols::canonical_sampling::MetropolisHastingsMover::add_backrub_mover ( core::Real  weight)

References add_mover().

void protocols::canonical_sampling::MetropolisHastingsMover::add_mover ( ThermodynamicMoverOP  mover,
core::Real  weight,
utility::tag::TagPtr const &  subtag 
)
virtual
void protocols::canonical_sampling::MetropolisHastingsMover::add_mover ( ThermodynamicMoverOP  mover,
core::Real  weight 
)
virtual

References movers_, and weighted_sampler_.

void protocols::canonical_sampling::MetropolisHastingsMover::add_observer ( ThermodynamicObserverOP  observer)

References observers_.

Referenced by parse_my_tag().

void protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover ( core::Real  weight)
void protocols::canonical_sampling::MetropolisHastingsMover::add_sidechain_mc_mover ( core::Real  weight,
core::Real  prob_uniform,
core::Real  prob_withinrot,
bool  preserve_cbeta,
core::Size  ntrials 
)
void protocols::canonical_sampling::MetropolisHastingsMover::add_sidechain_mover ( core::Real  weight,
core::Real  prob_uniform,
core::Real  prob_withinrot,
bool  preserve_cbeta 
)
void protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover ( core::Real  weight)
void protocols::canonical_sampling::MetropolisHastingsMover::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::canonical_sampling::MetropolisHastingsMover::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.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

bool protocols::canonical_sampling::MetropolisHastingsMover::finished ( ) const

References ntrials_, and trial_.

protocols::moves::MoverOP protocols::canonical_sampling::MetropolisHastingsMover::fresh_instance ( ) const
virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

References MetropolisHastingsMover().

std::string protocols::canonical_sampling::MetropolisHastingsMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

bool protocols::canonical_sampling::MetropolisHastingsMover::last_accepted ( ) const
inline
ThermodynamicMover const & protocols::canonical_sampling::MetropolisHastingsMover::last_move ( ) const
protocols::moves::MonteCarloCOP protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo ( ) const
ThermodynamicMoverOP protocols::canonical_sampling::MetropolisHastingsMover::mover_by_index ( numeric::Size  idx) const
inlineprotected

References movers_.

protocols::moves::MonteCarlo & protocols::canonical_sampling::MetropolisHastingsMover::nonconst_monte_carlo ( )
protected
core::Size protocols::canonical_sampling::MetropolisHastingsMover::ntrials ( ) const
inline
ObserverList const& protocols::canonical_sampling::MetropolisHastingsMover::observers ( )
inlineprotected
std::string protocols::canonical_sampling::MetropolisHastingsMover::output_file_name ( std::string const &  suffix,
bool  cumulate_jobs = false,
bool  cumulate_replicas = false 
) const
std::string const & protocols::canonical_sampling::MetropolisHastingsMover::output_name ( ) const
void protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

References add_mover(), add_observer(), protocols::moves::MoverFactory::get_instance(), monte_carlo_, protocols::moves::MoverFactory::newMover(), ntrials_, protocols::rosetta_scripts::parse_score_function(), set_tempering(), tempering_, and protocols::TR().

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::parse_my_tag().

core::Size protocols::canonical_sampling::MetropolisHastingsMover::prepare_simulation ( core::pose::Pose pose)
protected
ThermodynamicMoverOP protocols::canonical_sampling::MetropolisHastingsMover::random_mover ( )
virtual
bool protocols::canonical_sampling::MetropolisHastingsMover::reinitialize_for_each_job ( ) const
virtual

this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

bool protocols::canonical_sampling::MetropolisHastingsMover::reinitialize_for_new_input ( ) const
virtual

this function informs 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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

void protocols::canonical_sampling::MetropolisHastingsMover::set_last_accepted ( bool  setting)
inlineprotected
void protocols::canonical_sampling::MetropolisHastingsMover::set_last_move ( ThermodynamicMoverOP  setting)
protected
void protocols::canonical_sampling::MetropolisHastingsMover::set_monte_carlo ( protocols::moves::MonteCarloOP  monte_carlo)
void protocols::canonical_sampling::MetropolisHastingsMover::set_ntrials ( core::Size  ntrials)

References ntrials(), and ntrials_.

void protocols::canonical_sampling::MetropolisHastingsMover::set_output_name ( std::string const &  output_name)
void protocols::canonical_sampling::MetropolisHastingsMover::set_tempering ( TemperatureControllerOP  tempering)

References monte_carlo_, tempering(), and tempering_.

Referenced by parse_my_tag().

TemperatureControllerCOP protocols::canonical_sampling::MetropolisHastingsMover::tempering ( ) const
TemperatureControllerOP const& protocols::canonical_sampling::MetropolisHastingsMover::tempering ( )
inlineprotected

References tempering_.

void protocols::canonical_sampling::MetropolisHastingsMover::wind_down_simulation ( core::pose::Pose pose)
protected

Member Data Documentation

bool protocols::canonical_sampling::MetropolisHastingsMover::last_accepted_
private

Referenced by last_accepted(), and set_last_accepted().

ThermodynamicMoverOP protocols::canonical_sampling::MetropolisHastingsMover::last_move_
private

some status is necessary for the observers

Referenced by last_move(), and set_last_move().

protocols::moves::MonteCarloOP protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo_
private
utility::vector1< ThermodynamicMoverOP > protocols::canonical_sampling::MetropolisHastingsMover::movers_
private
core::Size protocols::canonical_sampling::MetropolisHastingsMover::ntrials_
private
utility::vector1< ThermodynamicObserverOP > protocols::canonical_sampling::MetropolisHastingsMover::observers_
private
std::string protocols::canonical_sampling::MetropolisHastingsMover::output_name_
private
bool protocols::canonical_sampling::MetropolisHastingsMover::output_name_from_job_distributor_
private
TemperatureControllerOP protocols::canonical_sampling::MetropolisHastingsMover::tempering_
private
core::Size protocols::canonical_sampling::MetropolisHastingsMover::trial_
private

Referenced by apply(), and finished().

numeric::random::WeightedSampler protocols::canonical_sampling::MetropolisHastingsMover::weighted_sampler_
private

Referenced by add_mover(), and random_mover().


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