Base class for recording a simulation trajectory. More...

#include <TrajectoryRecorder.hh>

Inheritance diagram for protocols::canonical_sampling::TrajectoryRecorder:

Public Member Functions
	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) 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	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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

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 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
virtual void	write_model (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMover const *metropolis_hastings_mover=nullptr)=0
	Pure virtual method called to write a model to the output file. 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 Member Functions
TrajectoryRecorder &	operator= (TrajectoryRecorder const &)=delete
	Assignment not allowed. More...

Private Attributes
core::Size	stride_

core::Size	model_count_

core::Size	step_count_

core::Size	cache_limit_

std::string	file_name_

bool	cumulate_jobs_

bool	cumulate_replicas_

Static Private Attributes
static bool	options_registered_

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

Base class for recording a simulation trajectory.

This class seems a little too geared towards file IO, which will make it awkward to create the database trajectory subclass that I want. But I'll get it to work one way or another.

Constructor & Destructor Documentation

protocols::canonical_sampling::TrajectoryRecorder::TrajectoryRecorder ( )

Default constructor.

References cache_limit_, cumulate_jobs_, cumulate_replicas_, file_name_, options_registered_, and stride_.

protocols::canonical_sampling::TrajectoryRecorder::~TrajectoryRecorder ( )

overridedefault

Destructor.

protocols::canonical_sampling::TrajectoryRecorder::TrajectoryRecorder ( TrajectoryRecorder const & )

default

Copy constructor.

Member Function Documentation

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

overridevirtual

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.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References update_after_boltzmann().

void protocols::canonical_sampling::TrajectoryRecorder::attributes_for_trajectory_recorder ( utility::tag::AttributeList & attlist )

static

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::provide_xml_schema(), protocols::canonical_sampling::PDBTrajectoryRecorder::provide_xml_schema(), and protocols::canonical_sampling::MetricRecorder::provide_xml_schema().

core::Size protocols::canonical_sampling::TrajectoryRecorder::cache_limit ( )

inline

Return the number of poses that can be cached.

References cache_limit_.

Referenced by protocols::canonical_sampling::DbTrajectoryRecorder::write_model().

void protocols::canonical_sampling::TrajectoryRecorder::cache_limit ( core::Size limit )

inline

Specify the maximum number of poses that can be cached.

This option can also be specified on the command line using the -trajectory:cache_limit flag. Note that some recorders don't use a cache at all, and will therefore ignore this option.

References cache_limit_.

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

inline

Return true if poses from different jobs will be written to the same trajectory file.

I suspect this is only meant to be used in the context of jd2. This option can only be set from the command line using the -trajectory:cumulate_jobs flag.

References cumulate_jobs_.

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

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

inline

Return true if poses from different replicas will be written to the same trajectory file.

I suspect this is only meant to be used in the context of jd2. This option can only be set from the command line using the -trajectory:cumulate_replicas flag.

References cumulate_replicas_.

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

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

inline

Return the file name for the trajectory.

References file_name_.

Referenced by protocols::coupled_moves::CoupledMovesProtocol::apply(), file_name(), protocols::canonical_sampling::PDBTrajectoryRecorder::PDBTrajectoryRecorder(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

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

inline

Set the file name for the trajectory.

References file_name(), and file_name_.

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

overridevirtual

Return the name of this mover.

Implements protocols::moves::Mover.

void protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover,
		core::Size	cycle
	)

overridevirtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References model_count_, protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo(), reset(), step_count_, and stride().

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::initialize_simulation(), and protocols::canonical_sampling::DbTrajectoryRecorder::initialize_simulation().

core::Size protocols::canonical_sampling::TrajectoryRecorder::model_count ( ) const

inline

Return the number of models that have been saved so far.

References model_count_.

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

void protocols::canonical_sampling::TrajectoryRecorder::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().

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis().

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

privatedelete

Assignment not allowed.

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

overridevirtual

Configure this mover from a RosettaScripts tag.

Reimplemented from protocols::moves::Mover.

References cache_limit_, cumulate_jobs_, cumulate_replicas_, file_name_, and stride_.

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::parse_my_tag(), and protocols::canonical_sampling::PDBTrajectoryRecorder::parse_my_tag().

void protocols::canonical_sampling::TrajectoryRecorder::register_options ( )

static

Associate relevant options with the TemperedDocking class.

References protocols::evaluation::options_registered_.

void protocols::canonical_sampling::TrajectoryRecorder::reset	(	protocols::moves::MonteCarlo const &	mc,
		protocols::canonical_sampling::MetropolisHastingsMover const *	metropolis_hastings_mover = `nullptr`
	)

virtual

Callback executed whenever the simulation is initialized or reset.

Reimplemented in protocols::canonical_sampling::PDBTrajectoryRecorder.

References model_count_, and step_count_.

Referenced by initialize_simulation(), and protocols::canonical_sampling::PDBTrajectoryRecorder::reset().

core::Size protocols::canonical_sampling::TrajectoryRecorder::step_count ( ) const

inline

Return the number of iterations that have occurred so far.

References step_count_.

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(), protocols::canonical_sampling::PDBTrajectoryRecorder::write_model(), and protocols::canonical_sampling::DbTrajectoryRecorder::write_model().

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

inline

Return how often models should be written to the trajectory.

References stride_.

Referenced by initialize_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(), and stride().

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

inline

Set how often models should be written to the trajectory.

This option can also be specified on the command line using the -trajectory:stride flag.

References stride(), and stride_.

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

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.

References model_count_, step_count_, stride_, and write_model().

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

void protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann ( protocols::moves::MonteCarlo const & mc )

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.

References protocols::moves::MonteCarlo::last_accepted_pose(), and update_after_boltzmann().

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