Manage the main loop of a canonical Monte Carlo simulation. More...

#include <MetropolisHastingsMover.hh>

Inheritance diagram for protocols::canonical_sampling::MetropolisHastingsMover:

Public Member Functions
	MetropolisHastingsMover ()
	Default constructor. More...

	MetropolisHastingsMover (MetropolisHastingsMover const &metropolis_hastings_mover)
	Copy constructor. More...

	~MetropolisHastingsMover () override
	Destructor. More...

void	apply (core::pose::Pose &pose) override
	Run the Metropolis-Hastings simulation. More...

protocols::moves::MoverOP	clone () const override
	Return the name of this mover. More...

protocols::moves::MoverOP	fresh_instance () const override
	Return a newly instantiated mover. More...

bool	reinitialize_for_each_job () const override
	Return false. This mover does not need to be reinitialized for each job. More...

bool	reinitialize_for_new_input () const override
	Return false. This mover does not need to be reinitialized for new input. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Use a RosettaScripts tag to configure this mover. More...

protocols::moves::MonteCarloCOP	monte_carlo () const
	Return the MonteCarlo object being used by this simulation. More...

void	set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo)
	Provide a MonteCarlo object to use for this simulation. More...

TemperatureControllerCOP	tempering () const
	Return the TemperatureController being used by this simulation. More...

void	set_tempering (TemperatureControllerOP)
	Provide a TemperatureController to use for this simulation. More...

core::Size	ntrials () const
	Return the number of iterations used by this simulation. More...

void	set_ntrials (core::Size ntrials)
	Set the number of iterations to use for this simulation. More...

core::Size	current_trial () const
	Return the iteration currently being processed by the simulation. More...

std::string const &	output_name () const
	Return the file name used by some of the observers to output data. More...

void	set_output_name (std::string const &output_name)
	Set the file name used by some of the observers to output data. More...

std::string	output_file_name (std::string const &suffix, bool cumulate_jobs=false, bool cumulate_replicas=false) const
	Return a file name that is consistent with the given options. More...

virtual ThermodynamicMoverOP	random_mover () const
	Return true if the simulation has been completed. More...

virtual void	add_mover (ThermodynamicMoverOP mover, core::Real weight, utility::tag::TagCOP const &subtag)
	Add the given mover to the simulation. More...

virtual void	add_mover (ThermodynamicMoverOP mover, core::Real weight)
	Add the given mover to the simulation. More...

void	add_backrub_mover (core::Real weight)
	Convenience method to add a backrub move to the simulation. More...

void	add_kic_mover (core::Real weight, protocols::loops::Loop const &loop)
	Convenience method to add a kinematic closure move to the simulation. More...

void	add_small_mover (core::Real weight)
	Convenience method to add a small move to the simulation. More...

void	add_shear_mover (core::Real weight)
	Convenience method to add a shear move to the simulation. More...

void	add_sidechain_mover (core::Real weight, core::Real prob_uniform, core::Real prob_withinrot, bool preserve_cbeta)
	Convenience method to add a sidechain move to the simulation. More...

void	add_sidechain_mc_mover (core::Real weight, core::Real prob_uniform, core::Real prob_withinrot, bool preserve_cbeta, core::Size ntrials)
	Convenience method to add a Monte Carlo sidechain move to the simulation. This move uses an internal Monte Carlo loop to generate a whole new set of sidechain conformations. More...

void	add_observer (ThermodynamicObserverOP observer)
	Add the given observer to this simulation. More...

ThermodynamicMover const &	last_move () const
	Return the most recently used ThermodynamicMover. More...

bool	last_accepted () const
	Return true if the last attempted move was accepted. More...

std::string	get_last_checkpoint () const

std::string	get_name () const override
	Each derived class must specify its name. The class name. 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...

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

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 Strings &	info ()
	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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	mover_or_add_group_name ()

static std::string	add_ct_name (std::string)

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
TemperatureControllerOP const &	tempering ()
	Protected non-const access to the TemperatureController. More...

ThermodynamicMoverOP	mover_by_index (numeric::Size idx) const
	Return the mover that was added at the given index. More...

void	write_checkpoint (core::pose::Pose const &pose)
	write checkpoint snapshots for restarting More...

bool	get_checkpoints ()
	get checkpoint_id for restarting More...

void	wind_down_simulation (core::pose::Pose &pose)
	Finalize all the movers and observers used in this simulation, and write some debrief statistics to the tracer. More...

core::Size	prepare_simulation (core::pose::Pose &pose)
	Initialize all the movers and observers to be used in this simulation. More...

void	set_last_accepted (bool setting)
	Indicate whether or not the last attempted move was accepted. More...

void	set_last_move (ThermodynamicMoverOP setting)
	Indicate what type of move was last attempted. More...

utility::vector1 < ThermodynamicObserverOP > const &	observers ()
	Return a list of all observers attached to this simulation. More...

protocols::moves::MonteCarlo &	nonconst_monte_carlo ()
	Protected non-const access to the MonteCarlo object. 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 Attributes
protocols::moves::MonteCarloOP	monte_carlo_

core::Size	ntrials_

core::Size	current_trial_

std::string	output_name_

utility::vector1 < ThermodynamicMoverOP >	movers_

utility::vector1 < ThermodynamicObserverOP >	observers_

TemperatureControllerOP	tempering_

numeric::random::WeightedSampler	weighted_sampler_

ThermodynamicMoverOP	last_move_

bool	last_accepted_

bool	output_name_from_job_distributor_

core::Size	checkpoint_count_

std::vector< std::string >	checkpoint_ids_

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

Detailed Description

Manage the main loop of a canonical Monte Carlo simulation.

To make the simulation flexible, most aspects of the algorithm have been delegated to other classes. Use the add_mover() methods to control which moves are used during the simulation. Use the set_tempering() method to control how the temperature changes during the simulation. This can be used to setup simulated annealing or parallel tempering runs. Management of the score function is delegated to the underlying MonteCarlo object, so use set_monte_carlo() to specify a score function. Use add_observer() to keep track of statistics and to record the trajectory.

Constructor & Destructor Documentation

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

Default constructor.

References protocols::checkpoint::checkpoint_with_interval().

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

Copy constructor.

References monte_carlo_, movers_, observers_, and tempering_.

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

overridedefault

Destructor.

Member Function Documentation

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

Convenience method to add a backrub move to the simulation.

References add_mover().

std::string protocols::canonical_sampling::MetropolisHastingsMover::add_ct_name ( std::string tag_name )

static

Referenced by provide_xml_schema().

void protocols::canonical_sampling::MetropolisHastingsMover::add_kic_mover	(	core::Real	weight,
		protocols::loops::Loop const &	loop
	)

Convenience method to add a kinematic closure move to the simulation.

References add_mover().

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

virtual

Add the given mover to the simulation.

In principle, information about the mover could be extracted from the given XML tag, but currently this function is a simple alias for add_mover().

Referenced by add_backrub_mover(), add_kic_mover(), add_shear_mover(), add_sidechain_mc_mover(), add_sidechain_mover(), add_small_mover(), and parse_my_tag().

void protocols::canonical_sampling::MetropolisHastingsMover::add_mover	(	ThermodynamicMoverOP	mover,
		core::Real	weight
	)

virtual

Add the given mover to the simulation.

Specify a weight to control how often this mover should be invoked. The weight does not have to be in any particular range. The probability of choosing any particular move will be the weight of that sampler divided by the sum of the weights of all the moves.

References movers_, and weighted_sampler_.

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

Add the given observer to this simulation.

References observers_.

Referenced by parse_my_tag().

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

Convenience method to add a shear move to the simulation.

References add_mover().

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
	)

Convenience method to add a Monte Carlo sidechain move to the simulation. This move uses an internal Monte Carlo loop to generate a whole new set of sidechain conformations.

References add_mover(), and monte_carlo_.

void protocols::canonical_sampling::MetropolisHastingsMover::add_sidechain_mover	(	core::Real	weight,
		core::Real	prob_uniform,
		core::Real	prob_withinrot,
		bool	preserve_cbeta
	)

Convenience method to add a sidechain move to the simulation.

References add_mover().

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

Convenience method to add a small move to the simulation.

References add_mover().

void protocols::canonical_sampling::MetropolisHastingsMover::apply ( core::pose::Pose & pose )

overridevirtual

Run the Metropolis-Hastings simulation.

Implements protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

References current_trial_, monte_carlo_, ntrials(), observers_, output_name_from_job_distributor_, prepare_simulation(), random_mover(), set_last_accepted(), set_last_move(), tempering_, protocols::canonical_sampling::tr(), wind_down_simulation(), and write_checkpoint().

protocols::moves::MoverOP protocols::canonical_sampling::MetropolisHastingsMover::clone ( ) const

overridevirtual

Return the name of this mover.

Return a copy of this mover.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

core::Size protocols::canonical_sampling::MetropolisHastingsMover::current_trial ( ) const

inline

Return the iteration currently being processed by the simulation.

References current_trial_.

Referenced by protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis(), and protocols::canonical_sampling::TemperingBase::observe_after_metropolis().

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

overridevirtual

Return a newly instantiated mover.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

bool protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints ( )

protected

get checkpoint_id for restarting

References core::io::silent::SilentFileData::begin(), checkpoint_count_, checkpoint_ids_, protocols::jd2::current_output_filename(), protocols::jd2::current_output_name(), protocols::jd2::current_replica(), core::io::silent::SilentFileData::filename(), core::io::silent::SilentFileData::read_file(), tempering_, and protocols::canonical_sampling::tr().

Referenced by prepare_simulation().

std::string protocols::canonical_sampling::MetropolisHastingsMover::get_last_checkpoint ( ) const

References checkpoint_ids_.

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), and protocols::canonical_sampling::BiasEnergy::restart_simulation().

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

References mover_name().

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

inline

Return true if the last attempted move was accepted.

References last_accepted_.

Referenced by protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis().

ThermodynamicMover const & protocols::canonical_sampling::MetropolisHastingsMover::last_move ( ) const

Return the most recently used ThermodynamicMover.

References last_move_.

Referenced by protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis().

protocols::moves::MonteCarloCOP protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo ( ) const

Return the MonteCarlo object being used by this simulation.

References monte_carlo_.

ThermodynamicMoverOP protocols::canonical_sampling::MetropolisHastingsMover::mover_by_index ( numeric::Size idx ) const

inlineprotected

Return the mover that was added at the given index.

References movers_.

std::string protocols::canonical_sampling::MetropolisHastingsMover::mover_name ( )

static

Referenced by get_name(), protocols::canonical_sampling::MetropolisHastingsMoverCreator::keyname(), parse_my_tag(), and provide_xml_schema().

std::string protocols::canonical_sampling::MetropolisHastingsMover::mover_or_add_group_name ( )

static

protocols::moves::MonteCarlo & protocols::canonical_sampling::MetropolisHastingsMover::nonconst_monte_carlo ( )

protected

Protected non-const access to the MonteCarlo object.

References monte_carlo_.

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

core::Size protocols::canonical_sampling::MetropolisHastingsMover::ntrials ( ) const

inline

Return the number of iterations used by this simulation.

References ntrials_.

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), apply(), protocols::canonical_sampling::ProgressBarObserver::observe_after_metropolis(), and set_ntrials().

utility::vector1< ThermodynamicObserverOP > const& protocols::canonical_sampling::MetropolisHastingsMover::observers ( )

inlineprotected

Return a list of all observers attached to this simulation.

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`,
		bool	cumulate_replicas = `false`
	)		const

Return a file name that is consistent with the given options.

If cumulate_jobs is true, the same filename will be returned for different jobs, so that the jobs all get cumulated in the same file. Likewise, if cumulate_replicas is true, the same filename will be returned for all replicas. If either of these options are set, MPI must be enabled.

References protocols::jd2::current_replica(), and output_name_.

Referenced by protocols::canonical_sampling::MetricRecorder::initialize_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

std::string const & protocols::canonical_sampling::MetropolisHastingsMover::output_name ( ) const

Return the file name used by some of the observers to output data.

References output_name_.

Referenced by protocols::canonical_sampling::TrialCounterObserver::finalize_simulation(), protocols::canonical_sampling::SimulatedTempering::finalize_simulation(), protocols::canonical_sampling::TemperingBase::finalize_simulation(), protocols::backrub::BackrubSidechainMover::finalize_simulation(), protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis(), protocols::canonical_sampling::TemperingBase::observe_after_metropolis(), prepare_simulation(), set_output_name(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

void protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Use a RosettaScripts tag to configure this mover.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::SidechainMetropolisHastingsMover.

References add_mover(), add_observer(), protocols::checkpoint::checkpoint_with_interval(), monte_carlo_, protocols::moves::MoverFactory::mover_creator_map(), mover_name(), protocols::moves::MoverFactory::newMover(), ntrials_, protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), set_tempering(), tempering_, and protocols::canonical_sampling::tr().

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

core::Size protocols::canonical_sampling::MetropolisHastingsMover::prepare_simulation ( core::pose::Pose & pose )

protected

Initialize all the movers and observers to be used in this simulation.

The return value indicates the number of cycles that have already been run, if the simulation is not being started or restarted. I'm not totally sure what this means though, and I couldn't see any way for this function to return anything other than 0. The necessary logic might be commented out right now.

References protocols::jd2::current_output_name(), get_checkpoints(), protocols::moves::Mover::get_self_ptr(), monte_carlo_, movers_, ntrials_, observers_, output_name(), output_name_from_job_distributor_, set_output_name(), tempering_, and protocols::canonical_sampling::tr().

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().

void protocols::canonical_sampling::MetropolisHastingsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References add_ct_name(), core::scoring::attributes_for_parse_score_function(), protocols::moves::complex_type_name_for_mover(), mover_name(), and protocols::moves::MoverFactory::mover_xml_schema_group_name().

Referenced by protocols::canonical_sampling::MetropolisHastingsMoverCreator::provide_xml_schema().

ThermodynamicMoverOP protocols::canonical_sampling::MetropolisHastingsMover::random_mover ( ) const

virtual

Return true if the simulation has been completed.

Return a randomly chosen mover to use in the next iteration.

You can control the probability of selecting a particular mover via the weight argument to the add_mover() method.

References movers_, core::scoring::rg, and weighted_sampler_.

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().

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

overridevirtual

Return false. This mover does not need to be reinitialized for each job.

Reimplemented from protocols::moves::Mover.

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

overridevirtual

Return false. This mover does not need to be reinitialized for new input.

Reimplemented from protocols::moves::Mover.

void protocols::canonical_sampling::MetropolisHastingsMover::set_last_accepted ( bool setting )

inlineprotected

Indicate whether or not the last attempted move was accepted.

References last_accepted_.

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().

void protocols::canonical_sampling::MetropolisHastingsMover::set_last_move ( ThermodynamicMoverOP setting )

protected

Indicate what type of move was last attempted.

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 )

Provide a MonteCarlo object to use for this simulation.

References monte_carlo(), monte_carlo_, and tempering_.

void protocols::canonical_sampling::MetropolisHastingsMover::set_ntrials ( core::Size ntrials )

Set the number of iterations to use for this simulation.

References ntrials(), and ntrials_.

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

Set the file name used by some of the observers to output data.

References output_name(), and output_name_.

Referenced by prepare_simulation(), and wind_down_simulation().

void protocols::canonical_sampling::MetropolisHastingsMover::set_tempering ( TemperatureControllerOP tempering )

Provide a TemperatureController to use for this simulation.

References monte_carlo_, tempering(), and tempering_.

Referenced by parse_my_tag().

TemperatureControllerCOP protocols::canonical_sampling::MetropolisHastingsMover::tempering ( ) const

Return the TemperatureController being used by this simulation.

References tempering_.

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::canonical_sampling::TrialCounterObserver::initialize_simulation(), set_tempering(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

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

inlineprotected

Protected non-const access to the TemperatureController.

References tempering_.

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

protected

Finalize all the movers and observers used in this simulation, and write some debrief statistics to the tracer.

References monte_carlo_, movers_, observers_, output_name_from_job_distributor_, set_output_name(), tempering_, and protocols::canonical_sampling::tr().

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), and apply().

void protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint ( core::pose::Pose const & pose )

protected

write checkpoint snapshots for restarting

References protocols::jd2::add_current_job_data_to_ss(), checkpoint_count_, checkpoint_ids_, protocols::jd2::current_output_filename(), protocols::jd2::current_output_name(), protocols::jd2::current_replica(), current_trial_, monte_carlo_, core::conformation::membrane::out, and protocols::kinmatch::str().

Referenced by apply().

Member Data Documentation

core::Size protocols::canonical_sampling::MetropolisHastingsMover::checkpoint_count_

private

Referenced by get_checkpoints(), and write_checkpoint().

std::vector< std::string > protocols::canonical_sampling::MetropolisHastingsMover::checkpoint_ids_

private

Referenced by get_checkpoints(), get_last_checkpoint(), and write_checkpoint().

core::Size protocols::canonical_sampling::MetropolisHastingsMover::current_trial_

private

Referenced by apply(), current_trial(), and write_checkpoint().

bool protocols::canonical_sampling::MetropolisHastingsMover::last_accepted_

private

Referenced by last_accepted(), and set_last_accepted().

ThermodynamicMoverOP protocols::canonical_sampling::MetropolisHastingsMover::last_move_

private

Referenced by last_move(), and set_last_move().

protocols::moves::MonteCarloOP protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo_

private

Referenced by add_sidechain_mc_mover(), apply(), MetropolisHastingsMover(), monte_carlo(), nonconst_monte_carlo(), parse_my_tag(), prepare_simulation(), set_monte_carlo(), set_tempering(), wind_down_simulation(), and write_checkpoint().

utility::vector1< ThermodynamicMoverOP > protocols::canonical_sampling::MetropolisHastingsMover::movers_

private

Referenced by add_mover(), MetropolisHastingsMover(), mover_by_index(), prepare_simulation(), random_mover(), and wind_down_simulation().

core::Size protocols::canonical_sampling::MetropolisHastingsMover::ntrials_

private

Referenced by ntrials(), parse_my_tag(), prepare_simulation(), and set_ntrials().

utility::vector1< ThermodynamicObserverOP > protocols::canonical_sampling::MetropolisHastingsMover::observers_

private

Referenced by add_observer(), apply(), MetropolisHastingsMover(), observers(), prepare_simulation(), and wind_down_simulation().

std::string protocols::canonical_sampling::MetropolisHastingsMover::output_name_

private

Referenced by output_file_name(), output_name(), and set_output_name().

bool protocols::canonical_sampling::MetropolisHastingsMover::output_name_from_job_distributor_

private

Referenced by apply(), prepare_simulation(), and wind_down_simulation().

TemperatureControllerOP protocols::canonical_sampling::MetropolisHastingsMover::tempering_

private

Referenced by apply(), get_checkpoints(), MetropolisHastingsMover(), parse_my_tag(), prepare_simulation(), set_monte_carlo(), set_tempering(), tempering(), and wind_down_simulation().

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:

src/protocols/canonical_sampling/MetropolisHastingsMover.hh
src/protocols/canonical_sampling/MetropolisHastingsMover.cc

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