Periodically output miscellaneous information. More...

#include <MetricRecorder.hh>

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

	~MetricRecorder ()
	Default destructor. More...

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

MetricRecorder &	operator= (MetricRecorder const &)
	Assignment operator. More...

virtual protocols::moves::MoverOP	clone () const
	Return a copy of this mover. More...

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

virtual std::string	get_name () const
	Return the name of this mover. 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)
	Use a RosettaScripts tag to configure this mover. More...

virtual bool	reinitialize_for_each_job () const
	Return true. This mover needs to be reinitialized for each job. More...

std::string const &	file_name () const
	Return the name of the file being written to. More...

void	file_name (std::string const &file_name)
	Set the name of the file being written to. More...

core::Size	stride () const
	Return the frequency with which data is written. More...

void	stride (core::Size stride)
	Set the frequency with which data is written. More...

bool	cumulate_jobs () const
	Return true if every job is being reported to the same file. More...

void	cumulate_jobs (bool cumulate_jobs)
	Indicate whether or not every job should be reported to the same file. More...

bool	cumulate_replicas () const
	Return true if every replica is being reported to the same file. More...

void	cumulate_replicas (bool cumulate_replicas)
	Indicate whether or not every replica should be reported to the same file. More...

bool	prepend_output_name () const
	Return true if the job name should be prepended onto the output filename. More...

void	prepend_output_name (bool prepend_output_name)
	Indicate whether or not the job name should be prepended onto the output filename. More...

void	add_torsion (core::id::TorsionID const &torsion_id, std::string name="")
	Include the given torsion in the output. More...

void	add_torsion (core::pose::Pose const &pose, std::string const &rsd, std::string type, core::Size torsion, std::string name="")
	Include the given torsion in the output. More...

void	reset (core::pose::Pose const &pose, MetropolisHastingsMoverCAP metropolis_hastings_mover=0)
	Truncate the output file and rewrite the output header. More...

void	update_after_boltzmann (core::pose::Pose const &pose, MetropolisHastingsMoverCAP metropolis_hastings_mover=0)
	Write information like temperature, score, and torsion angles to a file. More...

virtual void	apply (core::pose::Pose &pose)
	Just invoke update_after_boltzmann() with a const pose. More...

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

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

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

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...

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...

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...

Private Attributes
std::string	file_name_

core::Size	stride_

bool	cumulate_jobs_

bool	cumulate_replicas_

bool	prepend_output_name_

core::Size	step_count_

utility::io::ozstream	recorder_stream_

utility::vector1< std::pair < core::id::TorsionID, std::string > >	torsion_ids_

time_t	last_flush_

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

Periodically output miscellaneous information.

This class is capable of writing out a variety of data related to the trajectory. This includes the job name, the replica, the temperature, and the score. Any number of torsion angles can also be added to the report using add_torsion(). Methods are also provided for specifying an output filename. Most of the IO work is done by update_after_boltzmann().

Constructor & Destructor Documentation

protocols::canonical_sampling::MetricRecorder::MetricRecorder ( )

Default constructor.

Referenced by clone(), and fresh_instance().

protocols::canonical_sampling::MetricRecorder::~MetricRecorder ( )

Default destructor.

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

Copy constructor.

Member Function Documentation

void protocols::canonical_sampling::MetricRecorder::add_torsion	(	core::id::TorsionID const &	torsion_id,
		std::string	name = `""`
	)

Include the given torsion in the output.

References runtime_assert, torsion_ids_, and core::id::TorsionID::valid().

Referenced by add_torsion(), and parse_my_tag().

void protocols::canonical_sampling::MetricRecorder::add_torsion	(	core::pose::Pose const &	pose,
		std::string const &	rsd,
		std::string	type,
		core::Size	torsion,
		std::string	name = `""`
	)

Include the given torsion in the output.

References add_torsion(), core::id::BB, core::id::CHI, core::id::JUMP, core::pose::parse_resnum(), and utility_exit_with_message.

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

virtual

Just invoke update_after_boltzmann() with a const pose.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References update_after_boltzmann().

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

virtual

Return a copy of this mover.

Reimplemented from protocols::moves::Mover.

References MetricRecorder().

bool protocols::canonical_sampling::MetricRecorder::cumulate_jobs ( ) const

Return true if every job is being reported to the same file.

References cumulate_jobs_.

Referenced by cumulate_jobs().

void protocols::canonical_sampling::MetricRecorder::cumulate_jobs ( bool cumulate_jobs )

Indicate whether or not every job should be reported to the same file.

References cumulate_jobs(), and cumulate_jobs_.

bool protocols::canonical_sampling::MetricRecorder::cumulate_replicas ( ) const

Return true if every replica is being reported to the same file.

References cumulate_replicas_.

Referenced by cumulate_replicas().

void protocols::canonical_sampling::MetricRecorder::cumulate_replicas ( bool cumulate_replicas )

Indicate whether or not every replica should be reported to the same file.

References cumulate_replicas(), and cumulate_replicas_.

std::string const & protocols::canonical_sampling::MetricRecorder::file_name ( ) const

Return the name of the file being written to.

References file_name_.

Referenced by file_name(), and initialize_simulation().

void protocols::canonical_sampling::MetricRecorder::file_name ( std::string const & file_name )

Set the name of the file being written to.

References file_name(), and file_name_.

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

virtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References utility::io::ozstream::close(), and recorder_stream_.

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

virtual

Return a newly instantiated mover.

Reimplemented from protocols::moves::Mover.

References MetricRecorder().

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

virtual

Return the name of this mover.

Implements protocols::moves::Mover.

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

virtual

Callback executed before any Monte Carlo trials are attempted.

The cycle parameter gives the number of times that the simulation has been restarted. Since the restart feature is currently commented out, cycle should always be 0.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References cumulate_jobs_, cumulate_replicas_, file_name(), protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo(), protocols::canonical_sampling::MetropolisHastingsMover::output_file_name(), and reset().

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

virtual

Callback executed after the Metropolis criterion is evaluated.

Implements protocols::canonical_sampling::ThermodynamicObserver.

References protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo(), and update_after_boltzmann().

MetricRecorder & protocols::canonical_sampling::MetricRecorder::operator= ( MetricRecorder const & )

Assignment operator.

References runtime_assert.

void protocols::canonical_sampling::MetricRecorder::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

Use a RosettaScripts tag to configure this mover.

Reimplemented from protocols::moves::Mover.

References add_torsion(), cumulate_jobs_, cumulate_replicas_, file_name_, j, protocols::moves::Mover::name(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::nchi(), prepend_output_name_, core::pose::Pose::residue_type(), stride_, torsion(), core::pose::Pose::total_residue(), protocols::moves::Mover::type(), and utility_exit_with_message.

bool protocols::canonical_sampling::MetricRecorder::prepend_output_name ( ) const

Return true if the job name should be prepended onto the output filename.

References prepend_output_name_.

Referenced by prepend_output_name().

void protocols::canonical_sampling::MetricRecorder::prepend_output_name ( bool prepend_output_name )

Indicate whether or not the job name should be prepended onto the output filename.

References prepend_output_name(), and prepend_output_name_.

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

inlinevirtual

Return true. This mover needs to be reinitialized for each job.

Reimplemented from protocols::moves::Mover.

void protocols::canonical_sampling::MetricRecorder::reset	(	core::pose::Pose const &	pose,
		MetropolisHastingsMoverCAP	metropolis_hastings_mover = `0`
	)

Truncate the output file and rewrite the output header.

This method may not actually truncate the output file. It really just closes and reopens the file, and I'm not sure whether or not it picks a new name when it does the reopening.

References utility::io::ozstream::close(), recorder_stream_, step_count_, and update_after_boltzmann().

Referenced by initialize_simulation().

core::Size protocols::canonical_sampling::MetricRecorder::stride ( ) const

Return the frequency with which data is written.

References stride_.

Referenced by stride().

void protocols::canonical_sampling::MetricRecorder::stride ( core::Size stride )

Set the frequency with which data is written.

References stride(), and stride_.

void protocols::canonical_sampling::MetricRecorder::update_after_boltzmann	(	core::pose::Pose const &	pose,
		MetropolisHastingsMoverCAP	metropolis_hastings_mover = `0`
	)