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Rosetta 3.5
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#include <MetropolisHastingsMover.hh>


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) | |
| Mover & | operator= (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 Strings & | info () |
| 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::MonteCarlo & | nonconst_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... | |
Definition at line 45 of file MetropolisHastingsMover.hh.
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protected |
Definition at line 219 of file MetropolisHastingsMover.hh.
| protocols::canonical_sampling::MetropolisHastingsMover::MetropolisHastingsMover | ( | ) |
Definition at line 96 of file MetropolisHastingsMover.cc.
Referenced by fresh_instance().
| protocols::canonical_sampling::MetropolisHastingsMover::MetropolisHastingsMover | ( | MetropolisHastingsMover const & | metropolis_hastings_mover) |
Definition at line 102 of file MetropolisHastingsMover.cc.
References monte_carlo_, movers_, observers_, and tempering_.
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virtual |
Definition at line 127 of file MetropolisHastingsMover.cc.
| void protocols::canonical_sampling::MetropolisHastingsMover::add_backrub_mover | ( | core::Real | weight) |
Definition at line 451 of file MetropolisHastingsMover.cc.
References add_mover().
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virtual |
Definition at line 441 of file MetropolisHastingsMover.cc.
Referenced by add_backrub_mover(), add_shear_mover(), add_sidechain_mc_mover(), add_sidechain_mover(), add_small_mover(), and parse_my_tag().
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Definition at line 430 of file MetropolisHastingsMover.cc.
References movers_, and weighted_sampler_.
| void protocols::canonical_sampling::MetropolisHastingsMover::add_observer | ( | ThermodynamicObserverOP | observer) |
Definition at line 573 of file MetropolisHastingsMover.cc.
References observers_.
Referenced by parse_my_tag().
| void protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover | ( | core::Real | weight) |
Definition at line 487 of file MetropolisHastingsMover.cc.
References add_mover(), protocols::swa::rna::file_exists(), and core::kinematics::MoveMap::init_from_file().
| 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 | ||
| ) |
Definition at line 540 of file MetropolisHastingsMover.cc.
References add_mover(), monte_carlo_, and core::pack::task::TaskFactory::push_back().
| void protocols::canonical_sampling::MetropolisHastingsMover::add_sidechain_mover | ( | core::Real | weight, |
| core::Real | prob_uniform, | ||
| core::Real | prob_withinrot, | ||
| bool | preserve_cbeta | ||
| ) |
Definition at line 510 of file MetropolisHastingsMover.cc.
References add_mover(), and core::pack::task::TaskFactory::push_back().
| void protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover | ( | core::Real | weight) |
Definition at line 464 of file MetropolisHastingsMover.cc.
References add_mover(), protocols::swa::rna::file_exists(), and core::kinematics::MoveMap::init_from_file().
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virtual |
Implements protocols::moves::Mover.
Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.
Definition at line 185 of file MetropolisHastingsMover.cc.
References monte_carlo_, ntrials_, observers_, output_name_from_job_distributor_, prepare_simulation(), random_mover(), set_last_accepted(), set_last_move(), tempering_, protocols::TR(), trial_, and wind_down_simulation().
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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.
Definition at line 249 of file MetropolisHastingsMover.cc.
| bool protocols::canonical_sampling::MetropolisHastingsMover::finished | ( | ) | const |
Definition at line 365 of file MetropolisHastingsMover.cc.
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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.
Definition at line 255 of file MetropolisHastingsMover.cc.
References MetropolisHastingsMover().
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virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.
Definition at line 243 of file MetropolisHastingsMover.cc.
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inline |
Definition at line 192 of file MetropolisHastingsMover.hh.
References last_accepted_.
Referenced by protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis().
| ThermodynamicMover const & protocols::canonical_sampling::MetropolisHastingsMover::last_move | ( | ) | const |
Definition at line 418 of file MetropolisHastingsMover.cc.
References last_move_.
Referenced by protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis().
| protocols::moves::MonteCarloCOP protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo | ( | ) | const |
Definition at line 327 of file MetropolisHastingsMover.cc.
References monte_carlo_.
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::backrub::BackrubMover::initialize_simulation(), protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation(), protocols::canonical_sampling::MetricRecorder::initialize_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(), protocols::backrub::BackrubSidechainMover::observe_after_metropolis(), protocols::canonical_sampling::TrajectoryRecorder::observe_after_metropolis(), protocols::canonical_sampling::MetricRecorder::observe_after_metropolis(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis(), and set_monte_carlo().
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Definition at line 202 of file MetropolisHastingsMover.hh.
References movers_.
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Definition at line 331 of file MetropolisHastingsMover.cc.
References monte_carlo_.
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply().
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Definition at line 108 of file MetropolisHastingsMover.hh.
References ntrials_.
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and set_ntrials().
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Definition at line 220 of file MetropolisHastingsMover.hh.
References observers_.
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply().
| std::string protocols::canonical_sampling::MetropolisHastingsMover::output_file_name | ( | std::string const & | suffix, |
| bool | cumulate_jobs = false, |
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| bool | cumulate_replicas = false |
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| ) | const |
Definition at line 382 of file MetropolisHastingsMover.cc.
References protocols::jd2::current_replica(), and output_name_.
Referenced by protocols::canonical_sampling::MetricRecorder::initialize_simulation(), and protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation().
| std::string const & protocols::canonical_sampling::MetropolisHastingsMover::output_name | ( | ) | const |
Definition at line 370 of file MetropolisHastingsMover.cc.
References output_name_.
Referenced by protocols::canonical_sampling::TrialCounterObserver::finalize_simulation(), protocols::canonical_sampling::SimulatedTempering::finalize_simulation(), protocols::backrub::BackrubSidechainMover::finalize_simulation(), prepare_simulation(), and set_output_name().
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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.
Definition at line 267 of file MetropolisHastingsMover.cc.
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().
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Definition at line 130 of file MetropolisHastingsMover.cc.
References protocols::jd2::current_output_name(), protocols::jd2::JobDistributor::get_instance(), monte_carlo_, movers_, ntrials_, observers_, output_name(), output_name_from_job_distributor_, set_output_name(), tempering_, and protocols::TR().
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().
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Definition at line 424 of file MetropolisHastingsMover.cc.
References movers_, protocols::RG(), and weighted_sampler_.
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().
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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.
Definition at line 261 of file MetropolisHastingsMover.cc.
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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.
Definition at line 264 of file MetropolisHastingsMover.cc.
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Definition at line 213 of file MetropolisHastingsMover.hh.
References last_accepted_.
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().
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Definition at line 411 of file MetropolisHastingsMover.cc.
References last_move_.
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().
| void protocols::canonical_sampling::MetropolisHastingsMover::set_monte_carlo | ( | protocols::moves::MonteCarloOP | monte_carlo) |
Definition at line 336 of file MetropolisHastingsMover.cc.
References monte_carlo(), monte_carlo_, and tempering_.
| void protocols::canonical_sampling::MetropolisHastingsMover::set_ntrials | ( | core::Size | ntrials) |
Definition at line 358 of file MetropolisHastingsMover.cc.
| void protocols::canonical_sampling::MetropolisHastingsMover::set_output_name | ( | std::string const & | output_name) |
Definition at line 375 of file MetropolisHastingsMover.cc.
References output_name(), and output_name_.
Referenced by prepare_simulation(), and wind_down_simulation().
| void protocols::canonical_sampling::MetropolisHastingsMover::set_tempering | ( | TemperatureControllerOP | tempering) |
Definition at line 345 of file MetropolisHastingsMover.cc.
References monte_carlo_, tempering(), and tempering_.
Referenced by parse_my_tag().
| TemperatureControllerCOP protocols::canonical_sampling::MetropolisHastingsMover::tempering | ( | ) | const |
Definition at line 353 of file MetropolisHastingsMover.cc.
References tempering_.
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::canonical_sampling::TrialCounterObserver::initialize_simulation(), and set_tempering().
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Definition at line 199 of file MetropolisHastingsMover.hh.
References tempering_.
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Definition at line 220 of file MetropolisHastingsMover.cc.
References monte_carlo_, movers_, observers_, output_name_from_job_distributor_, set_output_name(), tempering_, and protocols::TR().
Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().
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Definition at line 238 of file MetropolisHastingsMover.hh.
Referenced by last_accepted(), and set_last_accepted().
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some status is necessary for the observers
Definition at line 237 of file MetropolisHastingsMover.hh.
Referenced by last_move(), and set_last_move().
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configurables...
Definition at line 226 of file MetropolisHastingsMover.hh.
Referenced by add_sidechain_mc_mover(), apply(), MetropolisHastingsMover(), monte_carlo(), nonconst_monte_carlo(), parse_my_tag(), prepare_simulation(), set_monte_carlo(), set_tempering(), and wind_down_simulation().
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Definition at line 229 of file MetropolisHastingsMover.hh.
Referenced by add_mover(), MetropolisHastingsMover(), mover_by_index(), prepare_simulation(), random_mover(), and wind_down_simulation().
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Definition at line 227 of file MetropolisHastingsMover.hh.
Referenced by apply(), finished(), ntrials(), parse_my_tag(), prepare_simulation(), and set_ntrials().
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Definition at line 230 of file MetropolisHastingsMover.hh.
Referenced by add_observer(), apply(), MetropolisHastingsMover(), observers(), prepare_simulation(), and wind_down_simulation().
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Definition at line 228 of file MetropolisHastingsMover.hh.
Referenced by output_file_name(), output_name(), and set_output_name().
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Definition at line 242 of file MetropolisHastingsMover.hh.
Referenced by apply(), prepare_simulation(), and wind_down_simulation().
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Definition at line 231 of file MetropolisHastingsMover.hh.
Referenced by apply(), MetropolisHastingsMover(), parse_my_tag(), prepare_simulation(), set_monte_carlo(), set_tempering(), tempering(), and wind_down_simulation().
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Definition at line 239 of file MetropolisHastingsMover.hh.
Referenced by apply(), and finished().
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Definition at line 234 of file MetropolisHastingsMover.hh.
Referenced by add_mover(), and random_mover().
1.8.4