#include <TemperatureController.hh>

Inheritance diagram for protocols::canonical_sampling::TemperatureController:

Collaboration diagram for protocols::canonical_sampling::TemperatureController:

Public Member Functions
	TemperatureController ()

	TemperatureController (TemperatureController const &)

virtual void	apply (core::pose::Pose &)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. 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	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	make a move in temperature space depending on the current score More...

virtual core::Real	temperature_move (core::Real score)=0
	execute the temperatur move ( called by observer_after_metropolis ) returns the current temperatur in kT. More...

virtual core::Real	temperature_move (core::pose::Pose &pose, core::Real score)
	second interface for temperature_move - standard implementation calls the pose-less temperature move. hamiltonian exchange needs to evaluate the alternative Hamiltonian though... More...

virtual core::Real	temperature () const =0

virtual core::Real	temperature (core::Size level) const =0
	return temperature of a certain level More...

virtual core::Size	temperature_level () const

virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size level, core::Real temperature, core::Size cycle)

virtual void	initialize_simulation (core::pose::Pose &, protocols::canonical_sampling::MetropolisHastingsMover const &, core::Size)

virtual core::Size	n_temp_levels () const

protocols::moves::MonteCarloCOP	monte_carlo () const

void	set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo)

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicObserver
	ThermodynamicObserver ()

virtual	~ThermodynamicObserver ()

virtual bool	restart_simulation (core::pose::Pose &, protocols::canonical_sampling::MetropolisHastingsMover &, core::Size &, core::Size &, core::Real &)
	callback executed before any Monte Carlo trials More...

virtual void	finalize_simulation (core::pose::Pose &, protocols::canonical_sampling::MetropolisHastingsMover const &)
	callback executed after all Monte Carlo trials More...

virtual bool	requires_pose ()
	return false here if a valid pose is not required for "observe" i.e. a trialcounter More...

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)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

virtual 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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Protected Member Functions
protocols::moves::MonteCarloOP	monte_carlo ()

Private Attributes
protocols::moves::MonteCarloOP	monte_carlo_

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...

Detailed Description

Definition at line 53 of file TemperatureController.hh.

Constructor & Destructor Documentation

protocols::canonical_sampling::TemperatureController::TemperatureController ( )

Definition at line 83 of file TemperatureController.cc.

protocols::canonical_sampling::TemperatureController::TemperatureController ( TemperatureController const & other)

Definition at line 87 of file TemperatureController.cc.

Member Function Documentation

virtual void protocols::canonical_sampling::TemperatureController::apply ( core::pose::Pose & )

inlinevirtual

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Reimplemented in protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::HamiltonianExchange, protocols::canonical_sampling::SimulatedTempering, and protocols::canonical_sampling::TemperingBase.

Definition at line 62 of file TemperatureController.hh.

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::FixedTemperatureController, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::HamiltonianExchange, protocols::canonical_sampling::SimulatedTempering, and protocols::canonical_sampling::TemperingBase.

Definition at line 125 of file TemperatureController.cc.

void protocols::canonical_sampling::TemperatureController::initialize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover,
		core::Size	level,
		core::Real	temperature,
		core::Size	cycle
	)

virtual

Reimplemented in protocols::canonical_sampling::HamiltonianExchange, and protocols::canonical_sampling::TemperingBase.

Definition at line 132 of file TemperatureController.cc.

virtual void protocols::canonical_sampling::TemperatureController::initialize_simulation	(	core::pose::Pose &	,
		protocols::canonical_sampling::MetropolisHastingsMover const &	,
		core::Size
	)

inlinevirtual

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Reimplemented in protocols::canonical_sampling::HamiltonianExchange, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::SimulatedTempering, and protocols::canonical_sampling::TemperingBase.

Definition at line 112 of file TemperatureController.hh.

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

Definition at line 100 of file TemperatureController.cc.

References monte_carlo_.

Referenced by protocols::canonical_sampling::TemperingBase::check_temp_consistency(), protocols::canonical_sampling::TemperingBase::initialize_simulation(), protocols::canonical_sampling::HamiltonianExchange::initialize_simulation(), protocols::canonical_sampling::TemperingBase::set_current_temp(), set_monte_carlo(), and protocols::canonical_sampling::TemperingBase::temperature().

protocols::moves::MonteCarloOP protocols::canonical_sampling::TemperatureController::monte_carlo ( )

protected

Definition at line 113 of file TemperatureController.cc.

References monte_carlo_.

virtual core::Size protocols::canonical_sampling::TemperatureController::n_temp_levels ( ) const

inlinevirtual

Reimplemented in protocols::canonical_sampling::TemperingBase.

Definition at line 118 of file TemperatureController.hh.

void protocols::canonical_sampling::TemperatureController::observe_after_metropolis ( protocols::canonical_sampling::MetropolisHastingsMover const & metropolis_hastings_mover)

virtual

make a move in temperature space depending on the current score

Implements protocols::canonical_sampling::ThermodynamicObserver.

Definition at line 94 of file TemperatureController.cc.

References monte_carlo_, and temperature_move().

virtual bool protocols::canonical_sampling::TemperatureController::reinitialize_for_each_job ( ) const

inlinevirtual

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 70 of file TemperatureController.hh.

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

inlinevirtual

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 74 of file TemperatureController.hh.

void protocols::canonical_sampling::TemperatureController::set_monte_carlo ( protocols::moves::MonteCarloOP monte_carlo)

Definition at line 105 of file TemperatureController.cc.

References monte_carlo(), and monte_carlo_.

virtual core::Real protocols::canonical_sampling::TemperatureController::temperature ( ) const

pure virtual

Implemented in protocols::canonical_sampling::FixedTemperatureController, and protocols::canonical_sampling::TemperingBase.

virtual core::Real protocols::canonical_sampling::TemperatureController::temperature ( core::Size level) const

pure virtual

return temperature of a certain level

Implemented in protocols::canonical_sampling::FixedTemperatureController, and protocols::canonical_sampling::TemperingBase.

virtual core::Size protocols::canonical_sampling::TemperatureController::temperature_level ( ) const

inlinevirtual

Reimplemented in protocols::canonical_sampling::TemperingBase.

Definition at line 96 of file TemperatureController.hh.

virtual core::Real protocols::canonical_sampling::TemperatureController::temperature_move ( core::Real score)

pure virtual

execute the temperatur move ( called by observer_after_metropolis ) returns the current temperatur in kT.

Implemented in protocols::canonical_sampling::FixedTemperatureController, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::HamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

Referenced by observe_after_metropolis(), and temperature_move().

core::Real protocols::canonical_sampling::TemperatureController::temperature_move	(	core::pose::Pose &	pose,
		core::Real	score
	)

virtual

second interface for temperature_move - standard implementation calls the pose-less temperature move. hamiltonian exchange needs to evaluate the alternative Hamiltonian though...

execute the temperatur move ( called by observer_after_metropolis ) returns the current temperatur in kT.

Reimplemented in protocols::canonical_sampling::HamiltonianExchange.

Definition at line 120 of file TemperatureController.cc.

References temperature_move().