Base class for reporting and recording data from a simulation. More...

#include <ThermodynamicObserver.hh>

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

virtual	~ThermodynamicObserver ()
	Destructor. More...

virtual void	apply (core::pose::Pose &)
	Callback executed after each move is made. More...

virtual void	initialize_simulation (core::pose::Pose &, MetropolisHastingsMover const &, core::Size)
	Callback executed before any Monte Carlo trials are attempted. More...

virtual void	observe_after_metropolis (MetropolisHastingsMover const &metropolis_hastings_mover)=0
	Callback executed after the Metropolis criterion is evaluated. More...

virtual void	finalize_simulation (core::pose::Pose &, MetropolisHastingsMover const &)
	Callback executed after all Monte Carlo trials are completed. 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)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

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

virtual std::string	get_name () const =0
	Each derived class must specify its name. The class name. 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 bool	reinitialize_for_each_job () const
	Inform 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
	Inform 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 MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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...

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 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. 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...

Detailed Description

Base class for reporting and recording data from a simulation.

Constructor & Destructor Documentation

protocols::canonical_sampling::ThermodynamicObserver::ThermodynamicObserver ( )

Default constructor.

protocols::canonical_sampling::ThermodynamicObserver::~ThermodynamicObserver ( )

virtual

Destructor.

Member Function Documentation

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

inlinevirtual

Callback executed after each move is made.

Even though the argument is a reference to a non-const pose, this method should not make any changes to the pose. Making changes to the pose is the role of the ThermodynamicMover class. The role of this class is to simply observe the poses being generated.

Implements protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::MetricRecorder, protocols::canonical_sampling::TrajectoryRecorder, protocols::canonical_sampling::TemperatureController, protocols::canonical_sampling::AsyncMPITemperingBase, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::TemperingBase, protocols::canonical_sampling::HamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

virtual void protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation	(	core::pose::Pose &	,
		MetropolisHastingsMover const &
	)

inlinevirtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented in protocols::canonical_sampling::MetricRecorder, protocols::canonical_sampling::BiasEnergy, protocols::canonical_sampling::TemperingBase, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::AsyncMPITemperingBase, protocols::canonical_sampling::SimulatedTempering, protocols::canonical_sampling::DbTrajectoryRecorder, protocols::canonical_sampling::PDBTrajectoryRecorder, and protocols::canonical_sampling::TrialCounterObserver.

Referenced by protocols::canonical_sampling::PDBTrajectoryRecorder::finalize_simulation(), and protocols::canonical_sampling::DbTrajectoryRecorder::finalize_simulation().

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

inlinevirtual

Callback executed before any Monte Carlo trials are attempted.

virtual void protocols::canonical_sampling::ThermodynamicObserver::observe_after_metropolis ( MetropolisHastingsMover const & metropolis_hastings_mover )

pure virtual

Callback executed after the Metropolis criterion is evaluated.

Implemented in protocols::canonical_sampling::MetricRecorder, protocols::canonical_sampling::TrajectoryRecorder, protocols::canonical_sampling::BiasEnergy, protocols::canonical_sampling::TemperatureController, protocols::canonical_sampling::TemperingBase, protocols::canonical_sampling::TrialCounterObserver, protocols::canonical_sampling::SilentTrajectoryRecorder, and protocols::canonical_sampling::ProgressBarObserver.

virtual bool protocols::canonical_sampling::ThermodynamicObserver::requires_pose ( )

inlinevirtual

Return false if this observer does not require a valid pose. TrialCounterObserver is an example of such an observer.

Reimplemented in protocols::canonical_sampling::TrialCounterObserver, and protocols::canonical_sampling::ProgressBarObserver.

virtual bool protocols::canonical_sampling::ThermodynamicObserver::restart_simulation	(	core::pose::Pose &	,
		MetropolisHastingsMover &	,
		core::Size &	,
		core::Size &	,
		core::Real &
	)

inlinevirtual

Attempt to restart the last simulation that was recorded by this observer.

For example, consider an observer that records trajectories. This method should open the file that was going to be written, read out the last pose in that trajectory, and assign it to the given pose reference so that the current trajectory can start from the same place. Other observers may help setup other parts of the simulation.

This is not a particularly robust system, because it may require several unrelated observers working in concert to properly reconstitute the simulation. In fact, the restart feature in MetropolisHastingsMover is currently commented out, so this method is never actually invoked. I would advise reimplementing this method to utility_exit_with_message() in any subclasses you write, so that you don't waste time writing an unused method but so you don't confuse anyone if this feature gets revived in the future.

Reimplemented in protocols::canonical_sampling::DbTrajectoryRecorder, and protocols::canonical_sampling::SilentTrajectoryRecorder.

The documentation for this class was generated from the following files:

src/protocols/canonical_sampling/ThermodynamicObserver.hh
src/protocols/canonical_sampling/ThermodynamicObserver.cc

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation