#include <SimulatedTempering.hh>

Inheritance diagram for protocols::canonical_sampling::SimulatedTempering:

Collaboration diagram for protocols::canonical_sampling::SimulatedTempering:

Public Member Functions
	SimulatedTempering ()

	SimulatedTempering (SimulatedTempering const &)

virtual void	apply (core::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 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...

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 ()

	TemperingBase (TemperingBase 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)

core::Real	temperature () const
	return current_temperature (in monte-carlo object) More...

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

core::Size	temperature_level () const

core::Size	n_temp_levels () const
	callback executed after all Monte Carlo trials More...

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

	TemperatureController (TemperatureController const &)

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::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...

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 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)

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

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::canonical_sampling::TemperingBase
static void	register_options ()

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)

Protected Member Functions inherited from protocols::canonical_sampling::TemperingBase
void	set_defaults ()
	handling of options including command-line More...

bool	check_temp_consistency ()

bool	time_for_temp_move ()

core::Size	current_temp ()

void	clear ()

void	set_temperatures (utility::vector1< core::Real > const &)

void	set_current_temp (core::Size new_temp)

bool	stats_line_output () const

bool	stats_silent_output () const

std::string const &	stats_file () const

void	generate_temp_range (core::Real temp_low, core::Real temp_high, core::Size n_levels, InterpolationType interpolation=linear)

Protected Member Functions inherited from protocols::canonical_sampling::TemperatureController
protocols::moves::MonteCarloOP	monte_carlo ()

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::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

Detailed Description

Definition at line 37 of file SimulatedTempering.hh.

Member Typedef Documentation

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

private

Definition at line 38 of file SimulatedTempering.hh.

Constructor & Destructor Documentation

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

Definition at line 105 of file SimulatedTempering.cc.

Referenced by fresh_instance().

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

Definition at line 109 of file SimulatedTempering.cc.

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

Member Function Documentation

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

inlinevirtual

Reimplemented from protocols::canonical_sampling::TemperingBase.

Definition at line 46 of file SimulatedTempering.hh.

protocols::moves::MoverOP protocols::canonical_sampling::SimulatedTempering::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.

Definition at line 230 of file SimulatedTempering.cc.

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.

Definition at line 164 of file SimulatedTempering.cc.

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)

Definition at line 173 of file SimulatedTempering.cc.

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

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.

Definition at line 236 of file SimulatedTempering.cc.

References SimulatedTempering().

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

virtual

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

Reimplemented from protocols::canonical_sampling::TemperingBase.

Definition at line 224 of file SimulatedTempering.cc.

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.

Definition at line 263 of file SimulatedTempering.cc.

References protocols::canonical_sampling::TemperingBase::init_from_options(), 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.

Definition at line 274 of file SimulatedTempering.cc.

References score_offset_, protocols::canonical_sampling::TemperingBase::set_temperatures(), protocols::canonical_sampling::tr(), 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.

Definition at line 129 of file SimulatedTempering.cc.

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::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::canonical_sampling::TemperingBase.

Definition at line 242 of file SimulatedTempering.cc.

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

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

static

Definition at line 76 of file SimulatedTempering.cc.

References 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

Definition at line 123 of file SimulatedTempering.cc.

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

Definition at line 149 of file SimulatedTempering.cc.

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

Definition at line 257 of file SimulatedTempering.cc.

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.

Definition at line 181 of file SimulatedTempering.cc.

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