#include <SimulatedTempering.hh>

Public Member Functions
	SimulatedTempering ()

	SimulatedTempering (SimulatedTempering const &)

virtual void	apply (core::pose::Pose &)
	No-op implemented only to satisfy the Mover interface. More...

virtual std::string	get_name () const
	Return the name of this class. More...

protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::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...

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

virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
	callback executed before any Monte Carlo trials More...

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

void	finalize_simulation (std::string const &output_name)

Public Member Functions inherited from protocols::canonical_sampling::TemperingBase
	TemperingBase ()
	Default constructor. More...

	TemperingBase (TemperingBase const &)
	Copy constructor. More...

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	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after the Metropolis criterion is evaluated. More...

core::Real	temperature () const
	Return the temperature of the underlying MonteCarlo object. More...

core::Real	temperature (core::Size level) const
	Return the temperature of the given level. More...

core::Size	temperature_level () const
	Return the current temperature level. More...

core::Size	n_temp_levels () const
	Return the number of temperature levels used by this controller. More...

Public Member Functions inherited from protocols::canonical_sampling::TemperatureController
	TemperatureController ()
	Default constructor. More...

	TemperatureController (TemperatureController const &)
	Copy constructor. More...

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

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

virtual core::Real	temperature_move (core::pose::Pose &pose)
	Execute a temperature move which depends on the current pose. More...

virtual GridCoord	level_2_grid_coord (core::Size level) const

virtual core::Size	exchange_grid_dim () const

virtual core::Size	nlevels_per_dim (core::Size) const

protocols::moves::MonteCarloCOP	monte_carlo () const
	Return const access to the MonteCarlo object being controlled. More...

virtual bool	finished_simulation (core::Size trials, core::Size ntrials)
	Return true if the simulation has been completed. More...

virtual void	set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo)
	Set the MonteCarlo object to be controlled. More...

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicObserver
	ThermodynamicObserver ()
	Default constructor. More...

virtual	~ThermodynamicObserver ()
	Destructor. More...

virtual bool	restart_simulation (core::pose::Pose &, MetropolisHastingsMover &, core::Size &, core::Size &, core::Real &)
	Attempt to restart the last simulation that was recorded by this observer. More...

virtual bool	requires_pose ()
	Return false if this observer does not require a valid pose. TrialCounterObserver is an example of such an observer. 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

void	set_type (std::string const &setting)

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

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::canonical_sampling::TemperingBase
static void	register_options ()
	Register the options used by this mover with the global options system. More...

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
void	set_defaults ()
	handling of options including command-line More...

virtual void	init_from_options ()
	Assigns user specified values to primitive members using command line options. More...

void	reweight ()
	update weights based on current counts More...

void	reset_raw_counter ()
	reset the raw counts per state (not the weighted ones) to 0 More...

virtual bool	initialize_from_file (std::string const &filename)
	initialize temperatures and weights from file, return false if IO error occurrs More...

virtual void	write_to_file (std::string const &file_in, std::string const &output_name, utility::vector1< core::Real > const &wcounts)
	Save temperatures and weights to a file. More...

Protected Member Functions inherited from protocols::canonical_sampling::TemperingBase
void	set_defaults ()
	Help the constructor initialize the object. More...

bool	check_temp_consistency ()
	Assert that the current temperature of the MonteCarlo object agrees with the current temperature level of this object. More...

virtual bool	time_for_temp_move ()
	Return true if a temperature move should be made on this iteration. More...

void	reset_temp_counter ()

core::Size	current_temp () const
	Return the current temperature level. Identical to temperature_level() as far as I can tell. More...

void	clear ()
	Forget all temperature levels and return to an uninitialized state. More...

void	set_temperatures (utility::vector1< core::Real > const &)
	Explicitly set the temperature levels. More...

virtual void	set_current_temp (core::Size new_temp)
	Set the temperature to the given level. More...

bool	stats_line_output () const
	Return true if a statistics summary should be written. More...

bool	stats_silent_output () const
	Return true if a statistics summary should be inserted into a silent file. More...

std::string const &	stats_file () const
	Return the name of the silent file into which statistics should be recorded. More...

void	generate_temp_range (core::Real temp_low, core::Real temp_high, core::Size n_levels, InterpolationType interpolation=linear)
	Explicitly set the temperature levels by interpolating the given parameters. More...

MultiTemperatureTrialCounter &	trial_counter ()

Protected Member Functions inherited from protocols::canonical_sampling::TemperatureController
protocols::moves::MonteCarloOP	monte_carlo ()
	Return non-const access to the MonteCarlo object being controlled. 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 Types
typedef TemperingBase	Parent

Private Attributes
core::Real	score_offset_
	----------—— member variables --------------------—— More...

core::Real	self_transition_

bool	temperature_jumps_

core::Size	reweight_stride_

utility::vector1< core::Real >	weights_
	-— state --— More...

utility::vector1< core::Size >	counts_

utility::vector1< core::Real >	weighted_counts_

core::Size	total_count_

Static Private Attributes
static bool	options_registered_
	---------------— register cmdline options ------------------------— More...

Additional Inherited Members
Public Types inherited from protocols::canonical_sampling::TemperatureController
typedef utility::vector1 < core::Size >	GridCoord

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Protected Attributes inherited from protocols::canonical_sampling::TemperingBase
utility::vector1< core::Real >	temperatures_
	Temperature levels. More...

core::Size	temperature_stride_
	Frequency for attempting temperature moves (e.g. once every `io_stride_` steps). More...

core::Size	io_stride_
	Frequency with which statistics should be written (e.g. once every `io_stride_` steps). More...

bool	trust_current_temp_
	If false, look for current temperature in monte_carlo_ before each move. Set to true by default. More...

bool	stats_line_output_
	If true, a statistics summary will be written. More...

bool	stats_silent_output_
	If true, the statistics summary will be inserted in a silent file. More...

std::string	stats_file_
	Name of the silent file used for writing statistics. More...

protocols::jd2::JobOP	job_
	Job object to report on temperatures. More...

bool	instance_initialized_
	If false, init_from_options() will be called before the simulation starts. More...

core::Size	current_temp_
	Current temperature level. Not the current temperature! More...

core::Size	temp_trial_count_
	Number of times time_for_temp_move() has been called. This method is meant to be called every time temperature_move() is called. More...

MultiTemperatureTrialCounter	trial_counter_

Detailed Description

The only way to set the temperature range used for simulated annealing is to use the command line. The relevant options are:

-tempering::temp::range <low> <high>

-tempering::temp::low <low> -tempering::temp::high <high>

Member Typedef Documentation

typedef TemperingBase protocols::canonical_sampling::SimulatedTempering::Parent

private

Constructor & Destructor Documentation

protocols::canonical_sampling::SimulatedTempering::SimulatedTempering ( )

Referenced by fresh_instance().

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

References canonical_sampling, counts_, score_offset_, self_transition_, weighted_counts_, and weights_.

Member Function Documentation

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

inlinevirtual

No-op implemented only to satisfy the Mover interface.

Reimplemented from protocols::canonical_sampling::TemperingBase.

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

virtual

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.

void protocols::canonical_sampling::SimulatedTempering::finalize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover
	)

virtual

callback executed after all Monte Carlo trials

Reimplemented from protocols::canonical_sampling::TemperingBase.

References protocols::canonical_sampling::TemperingBase::finalize_simulation(), and protocols::canonical_sampling::MetropolisHastingsMover::output_name().

void protocols::canonical_sampling::SimulatedTempering::finalize_simulation ( std::string const & output_name )

References reset_raw_counter(), reweight(), protocols::canonical_sampling::TemperingBase::stats_file(), weighted_counts_, and write_to_file().

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

virtual

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.

References SimulatedTempering().

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

virtual

Return the name of this class.

Reimplemented from protocols::canonical_sampling::TemperingBase.

void protocols::canonical_sampling::SimulatedTempering::init_from_options ( )

protectedvirtual

Assigns user specified values to primitive members using command line options.

Reimplemented from protocols::canonical_sampling::TemperingBase.

References protocols::canonical_sampling::TemperingBase::init_from_options(), option, reweight_stride_, score_offset_, temperature_jumps_, and protocols::canonical_sampling::tr.

bool protocols::canonical_sampling::SimulatedTempering::initialize_from_file ( std::string const & filename )

protectedvirtual

initialize temperatures and weights from file, return false if IO error occurrs

Reimplemented from protocols::canonical_sampling::TemperingBase.

References getline(), utility::io::izstream::good(), in, score_offset_, protocols::canonical_sampling::TemperingBase::set_temperatures(), tag, protocols::canonical_sampling::tr, weight, weighted_counts_, and weights_.

void protocols::canonical_sampling::SimulatedTempering::initialize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover,
		core::Size	cycle
	)

virtual

callback executed before any Monte Carlo trials

Reimplemented from protocols::canonical_sampling::TemperingBase.

References protocols::canonical_sampling::TemperingBase::initialize_simulation(), protocols::canonical_sampling::TemperingBase::n_temp_levels(), reset_raw_counter(), total_count_, protocols::canonical_sampling::tr, weighted_counts_, and weights_.

void protocols::canonical_sampling::SimulatedTempering::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::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::canonical_sampling::TemperingBase.

References protocols::canonical_sampling::TemperingBase::parse_my_tag(), reweight_stride_, score_offset_, and temperature_jumps_.

void protocols::canonical_sampling::SimulatedTempering::register_options ( )

static

References NEW_OPT, protocols::evaluation::options_registered_, and protocols::evaluation::register_options().

Referenced by protocols::docking::TemperedDocking::register_options().

void protocols::canonical_sampling::SimulatedTempering::reset_raw_counter ( )

protected

reset the raw counts per state (not the weighted ones) to 0

callback executed before any Monte Carlo trials use to fill count_ with 0

References counts_, and protocols::canonical_sampling::TemperingBase::n_temp_levels().

Referenced by finalize_simulation(), initialize_simulation(), and temperature_move().

void protocols::canonical_sampling::SimulatedTempering::reweight ( )

protected

update weights based on current counts

References counts_, weighted_counts_, and weights_.

Referenced by finalize_simulation(), and temperature_move().

void protocols::canonical_sampling::SimulatedTempering::set_defaults ( )

protected

handling of options including command-line

References score_offset_, and self_transition_.

core::Real protocols::canonical_sampling::SimulatedTempering::temperature_move ( core::Real score )

virtual

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

Implements protocols::canonical_sampling::TemperatureController.

void protocols::canonical_sampling::SimulatedTempering::write_to_file	(	std::string const &	file_in,
		std::string const &	output_name,
		utility::vector1< core::Real > const &	wcounts
	)