Record a trajectory to the rosetta-specific silent file format. More...

#include <SilentTrajectoryRecorder.hh>

Inheritance diagram for protocols::canonical_sampling::SilentTrajectoryRecorder:

Public Types
typedef TrajectoryRecorder	Parent

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

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

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

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

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

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) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...

bool	restart_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover &metropolis_hastings_mover, core::Size &cycle, core::Size &temp_level, core::Real &temperature) override
	Attempt to restart the last simulation that was recorded by this observer. 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::TrajectoryRecorder
	TrajectoryRecorder ()
	Default constructor. More...

	~TrajectoryRecorder () override
	Destructor. More...

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

std::string	get_name () const override
	Return the name of this mover. More...

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) override
	Configure this mover from a RosettaScripts tag. More...

std::string const &	file_name () const
	Return the file name for the trajectory. More...

void	file_name (std::string const &file_name)
	Set the file name for the trajectory. More...

core::Size	model_count () const
	Return the number of models that have been saved so far. More...

core::Size	step_count () const
	Return the number of iterations that have occurred so far. More...

core::Size	stride () const
	Return how often models should be written to the trajectory. More...

void	stride (core::Size stride)
	Set how often models should be written to the trajectory. More...

core::Size	cache_limit ()
	Return the number of poses that can be cached. More...

void	cache_limit (core::Size limit)
	Specify the maximum number of poses that can be cached. More...

bool	cumulate_jobs () const
	Return true if poses from different jobs will be written to the same trajectory file. More...

bool	cumulate_replicas () const
	Return true if poses from different replicas will be written to the same trajectory file. More...

virtual void	reset (protocols::moves::MonteCarlo const &mc, protocols::canonical_sampling::MetropolisHastingsMover const *metropolis_hastings_mover=nullptr)
	Callback executed whenever the simulation is initialized or reset. More...

void	update_after_boltzmann (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMover const *metropolis_hastings_mover=nullptr)
	Callback executed after each move is made. More...

void	update_after_boltzmann (protocols::moves::MonteCarlo const &mc)
	Callback executed after each move is made. More...

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

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

	~ThermodynamicObserver () override
	Destructor. More...

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

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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static void	register_options ()
	Associates relevant options with the TemperedDocking class. More...

static std::string	mover_name ()

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

Static Public Member Functions inherited from protocols::canonical_sampling::TrajectoryRecorder
static void	register_options ()
	Associate relevant options with the TemperedDocking class. More...

static void	attributes_for_trajectory_recorder (utility::tag::AttributeList &)

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	write_model (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMover const *metropolis_hastings_mover=nullptr) override
	Append the given model to the silent file trajectory being written. 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...

Protected Attributes
core::Size	score_stride_

Static Protected Attributes
static bool	options_registered_

Private Attributes
protocols::jd2::JobOutputterOP	job_outputter_

Detailed Description

Record a trajectory to the rosetta-specific silent file format.

Member Typedef Documentation

typedef TrajectoryRecorder protocols::canonical_sampling::SilentTrajectoryRecorder::Parent

Constructor & Destructor Documentation

protocols::canonical_sampling::SilentTrajectoryRecorder::SilentTrajectoryRecorder ( )

Default constructor.

References protocols::evaluation::options_registered_.

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

Copy constructor.

Member Function Documentation

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

overridevirtual

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.

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

overridevirtual

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.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::canonical_sampling::SilentTrajectoryRecorder::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 protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation(), and protocols::canonical_sampling::tr().

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

static

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

void protocols::canonical_sampling::SilentTrajectoryRecorder::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::jd2::get_string_real_pairs_from_current_job(), protocols::moves::MonteCarlo::last_accepted_pose(), protocols::mean_field::max(), protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo(), protocols::canonical_sampling::TrajectoryRecorder::observe_after_metropolis(), protocols::moves::MonteCarlo::show_counters(), protocols::canonical_sampling::TrajectoryRecorder::step_count(), protocols::canonical_sampling::TrajectoryRecorder::stride(), and protocols::canonical_sampling::tr().

void protocols::canonical_sampling::SilentTrajectoryRecorder::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
	)

overridevirtual

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::moves::Mover.

References job_outputter_, protocols::canonical_sampling::TrajectoryRecorder::parse_my_tag(), and score_stride_.

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

static

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

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

void protocols::canonical_sampling::SilentTrajectoryRecorder::register_options ( )

static

Associates relevant options with the TemperedDocking class.

References protocols::evaluation::options_registered_, and protocols::moves::Mover::register_options().

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

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

overridevirtual

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 from protocols::canonical_sampling::ThermodynamicObserver.

References core::pose::Pose::add_constraints(), core::io::silent::SilentFileData::begin(), core::pose::Pose::constraint_set(), protocols::jd2::current_output_name(), protocols::jd2::current_replica(), core::pose::Pose::data(), core::io::silent::SilentFileData::filename(), protocols::canonical_sampling::MetropolisHastingsMover::get_last_checkpoint(), core::io::silent::SilentFileData::matched_tags(), core::io::silent::SilentFileData::read_file(), core::io::silent::SilentFileData::size(), and protocols::canonical_sampling::tr().

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