Periodically output miscellaneous information. More...

#include <MetricRecorder.hh>

Inheritance diagram for protocols::canonical_sampling::MetricRecorder:

[legend]

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

	~MetricRecorder () override
	Default destructor. More...

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

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

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Return the name of this mover. More...

bool	reinitialize_for_each_job () const override
	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 const &name="")
	Include the given torsion in the output. More...

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

void	add_torsion (TorsionSpec const &torsion)

void	reset (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMover const *metropolis_hastings_mover=nullptr)
	Truncate the output file and rewrite the output header. More...

void	update_after_boltzmann (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMover const *metropolis_hastings_mover=nullptr)
	Write information like temperature, score, and torsion angles to a file. More...

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

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

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

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

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

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

	~ThermodynamicObserver () override
	Destructor. More...

void	apply (core::pose::Pose &) override
	Callback executed after each move is made. 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 MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

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

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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	add_torsion (utility::vector1< std::pair< core::id::TorsionID, std::string > > &torsion_ids, core::Size rsd, std::string type, core::Size torsion, std::string const &name="") const

utility::vector1< std::pair< core::id::TorsionID, std::string > >	get_torsion_ids (core::pose::Pose const &pose) const
	Expand the list of torsion ids based on the Pose. 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 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_

utility::vector1< TorsionSpec >	torsion_specs_

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 std::list< std::string >	Strings

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

◆ MetricRecorder() [1/2]

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

Default constructor.

◆ ~MetricRecorder()

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

overridedefault

Default destructor.

◆ MetricRecorder() [2/2]

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

Copy constructor.

Member Function Documentation

◆ add_torsion() [1/4]

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

Include the given torsion in the output.

References protocols::moves::Mover::name(), core::id::TorsionID::str(), torsion_ids_, and core::id::TorsionID::valid().

Referenced by add_torsion(), get_torsion_ids(), and parse_my_tag().

◆ add_torsion() [2/4]

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

Include the given torsion in the output.

References add_torsion(), protocols::moves::Mover::name(), core::pose::parse_resnum(), torsion_ids_, and protocols::moves::Mover::type().

◆ add_torsion() [3/4]

void protocols::canonical_sampling::MetricRecorder::add_torsion ( TorsionSpec const & torsion )

References torsion_specs_.

◆ add_torsion() [4/4]

void protocols::canonical_sampling::MetricRecorder::add_torsion	(	utility::vector1< std::pair< core::id::TorsionID, std::string > > &	torsion_ids,
		core::Size	rsd,
		std::string	type,
		core::Size	torsion,
		std::string const &	name = `""`
	)		const

protected

References core::id::BB, core::id::CHI, core::id::JUMP, protocols::moves::Mover::name(), core::id::TorsionID::str(), protocols::moves::Mover::type(), and core::id::TorsionID::valid().

◆ apply()

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

overridevirtual

Just invoke update_after_boltzmann() with a const pose.

Implements protocols::moves::Mover.

References update_after_boltzmann().

◆ clone()

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

overridevirtual

Return a copy of this mover.

Reimplemented from protocols::moves::Mover.

◆ cumulate_jobs() [1/2]

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().

◆ cumulate_jobs() [2/2]

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_.

◆ cumulate_replicas() [1/2]

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().

◆ cumulate_replicas() [2/2]

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_.

◆ file_name() [1/2]

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().

◆ file_name() [2/2]

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_.

◆ finalize_simulation()

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

overridevirtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References recorder_stream_.

◆ fresh_instance()

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

overridevirtual

Return a newly instantiated mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_torsion_ids()

utility::vector1< std::pair< core::id::TorsionID, std::string > > protocols::canonical_sampling::MetricRecorder::get_torsion_ids ( core::pose::Pose const & pose ) const

protected

Expand the list of torsion ids based on the Pose.

References add_torsion(), protocols::canonical_sampling::AllBB, protocols::canonical_sampling::AllChi, core::chemical::ResidueTypeBase::name3(), core::pose::parse_resnum(), core::pose::Pose::residue_type(), protocols::canonical_sampling::Single, core::pose::Pose::size(), core::id::to_string(), torsion_ids_, and torsion_specs_.

Referenced by update_after_boltzmann().

◆ initialize_simulation()

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

overridevirtual

Callback executed before any Monte Carlo trials are attempted.

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().

◆ mover_name()

std::string protocols::canonical_sampling::MetricRecorder::mover_name ( )

static

Referenced by get_name(), protocols::canonical_sampling::MetricRecorderCreator::keyname(), and provide_xml_schema().

◆ observe_after_metropolis()

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

overridevirtual

Callback executed after the Metropolis criterion is evaluated.

Implements protocols::canonical_sampling::ThermodynamicObserver.

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

◆ operator=()

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

delete

Assignment operator.

◆ parse_my_tag()

void protocols::canonical_sampling::MetricRecorder::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Return the name of this mover.

Use a RosettaScripts tag to configure this mover.

Reimplemented from protocols::moves::Mover.

References add_torsion(), protocols::canonical_sampling::AllBB, protocols::canonical_sampling::AllChi, cumulate_jobs_, cumulate_replicas_, file_name_, protocols::canonical_sampling::TorsionSpec::name, protocols::canonical_sampling::TorsionSpec::number, prepend_output_name_, protocols::canonical_sampling::TorsionSpec::rsd, protocols::canonical_sampling::Single, stride_, protocols::canonical_sampling::TorsionSpec::style, and protocols::canonical_sampling::TorsionSpec::type.

◆ prepend_output_name() [1/2]

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().

◆ prepend_output_name() [2/2]

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_.

◆ provide_xml_schema()

void protocols::canonical_sampling::MetricRecorder::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::canonical_sampling::TrajectoryRecorder::attributes_for_trajectory_recorder(), protocols::moves::complex_type_name_for_mover(), and mover_name().

Referenced by protocols::canonical_sampling::MetricRecorderCreator::provide_xml_schema().

◆ reinitialize_for_each_job()

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

inlineoverridevirtual

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

Reimplemented from protocols::moves::Mover.

◆ reset()

void protocols::canonical_sampling::MetricRecorder::reset	(	core::pose::Pose const &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const *	metropolis_hastings_mover = `nullptr`
	)

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 recorder_stream_, step_count_, and update_after_boltzmann().

Referenced by initialize_simulation().

◆ stride() [1/2]

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

Return the frequency with which data is written.

References stride_.

Referenced by stride().

◆ stride() [2/2]

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

Set the frequency with which data is written.

References stride(), and stride_.

◆ update_after_boltzmann()

void protocols::canonical_sampling::MetricRecorder::update_after_boltzmann	(	core::pose::Pose const &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const *	metropolis_hastings_mover = `nullptr`
	)

Write information like temperature, score, and torsion angles to a file.

References cumulate_jobs_, cumulate_replicas_, protocols::jd2::current_nstruct_index(), protocols::jd2::current_output_name(), protocols::jd2::current_replica(), core::pose::Pose::energies(), file_name_, get_torsion_ids(), protocols::jd2::jd2_used(), last_flush_, protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo(), protocols::canonical_sampling::MetropolisHastingsMover::output_name(), prepend_output_name_, recorder_stream_, step_count_, stride_, protocols::canonical_sampling::MetropolisHastingsMover::tempering(), core::pose::Pose::torsion(), and core::scoring::Energies::total_energy().

Referenced by apply(), observe_after_metropolis(), and reset().

Member Data Documentation

◆ cumulate_jobs_

bool protocols::canonical_sampling::MetricRecorder::cumulate_jobs_

private

Referenced by cumulate_jobs(), initialize_simulation(), parse_my_tag(), and update_after_boltzmann().

◆ cumulate_replicas_

bool protocols::canonical_sampling::MetricRecorder::cumulate_replicas_

private

Referenced by cumulate_replicas(), initialize_simulation(), parse_my_tag(), and update_after_boltzmann().

◆ file_name_

std::string protocols::canonical_sampling::MetricRecorder::file_name_

private

Referenced by file_name(), parse_my_tag(), and update_after_boltzmann().

◆ last_flush_

time_t protocols::canonical_sampling::MetricRecorder::last_flush_

private

Referenced by update_after_boltzmann().

◆ prepend_output_name_

bool protocols::canonical_sampling::MetricRecorder::prepend_output_name_

private

Referenced by parse_my_tag(), prepend_output_name(), and update_after_boltzmann().

◆ recorder_stream_

utility::io::ozstream protocols::canonical_sampling::MetricRecorder::recorder_stream_

private

Referenced by finalize_simulation(), reset(), and update_after_boltzmann().

◆ step_count_

core::Size protocols::canonical_sampling::MetricRecorder::step_count_

private

Referenced by reset(), and update_after_boltzmann().

◆ stride_

core::Size protocols::canonical_sampling::MetricRecorder::stride_

private

Referenced by parse_my_tag(), stride(), and update_after_boltzmann().

◆ torsion_ids_

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

private

Referenced by add_torsion(), and get_torsion_ids().

◆ torsion_specs_

utility::vector1< TorsionSpec > protocols::canonical_sampling::MetricRecorder::torsion_specs_

private

Referenced by add_torsion(), and get_torsion_ids().

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

src/protocols/canonical_sampling/MetricRecorder.hh
src/protocols/canonical_sampling/MetricRecorder.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MetricRecorder() [1/2]

◆ ~MetricRecorder()

◆ MetricRecorder() [2/2]

Member Function Documentation

◆ add_torsion() [1/4]

◆ add_torsion() [2/4]

◆ add_torsion() [3/4]

◆ add_torsion() [4/4]

◆ apply()

◆ clone()

◆ cumulate_jobs() [1/2]

◆ cumulate_jobs() [2/2]

◆ cumulate_replicas() [1/2]

◆ cumulate_replicas() [2/2]

◆ file_name() [1/2]

◆ file_name() [2/2]

◆ finalize_simulation()

◆ fresh_instance()

◆ get_name()

◆ get_torsion_ids()

◆ initialize_simulation()

◆ mover_name()

◆ observe_after_metropolis()

◆ operator=()

◆ parse_my_tag()

◆ prepend_output_name() [1/2]

◆ prepend_output_name() [2/2]

◆ provide_xml_schema()

◆ reinitialize_for_each_job()

◆ reset()

◆ stride() [1/2]

◆ stride() [2/2]

◆ update_after_boltzmann()

Member Data Documentation

◆ cumulate_jobs_

◆ cumulate_replicas_

◆ file_name_

◆ last_flush_

◆ prepend_output_name_

◆ recorder_stream_

◆ step_count_

◆ stride_

◆ torsion_ids_

◆ torsion_specs_