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

#include <TrajectoryRecorder.hh>

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

	~TrajectoryRecorder ()
	Destructor. More...

	TrajectoryRecorder (TrajectoryRecorder const &)
	Copy constructor. 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)
	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, MetropolisHastingsMoverCAP metropolis_hastings_mover=0)
	Callback executed whenever the simulation is initialized or reset. More...

void	update_after_boltzmann (core::pose::Pose const &pose, MetropolisHastingsMoverCAP metropolis_hastings_mover=0)
	Save the given pose to the trajectory. More...

void	update_after_boltzmann (protocols::moves::MonteCarlo const &mc)
	Save the given pose to the trajectory. More...

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

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

virtual	~ThermodynamicObserver ()
	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	~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)

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

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

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, MetropolisHastingsMoverCAP metropolis_hastings_mover=0)=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 &)
	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 protocols::filters::Filters_map	Filters_map

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_, option, options_registered_, and stride_.

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

Destructor.

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

Copy constructor.

Member Function Documentation

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

virtual

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().

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::restart_simulation(), 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::restart_simulation(), 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 file_name(), protocols::canonical_sampling::PDBTrajectoryRecorder::PDBTrajectoryRecorder(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), 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

virtual

Return the name of this mover.

Implements protocols::moves::Mover.

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

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

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.

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

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 ( MetropolisHastingsMover const & metropolis_hastings_mover )

virtual

Callback executed after the Metropolis criterion is evaluated.

Implements protocols::canonical_sampling::ThermodynamicObserver.

Reimplemented in protocols::canonical_sampling::SilentTrajectoryRecorder.

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 & )

private

Assignment not allowed.

References runtime_assert.

void protocols::canonical_sampling::TrajectoryRecorder::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

Configure this mover from a RosettaScripts tag.

Reimplemented from protocols::moves::Mover.

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

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 NEW_OPT, and protocols::evaluation::options_registered_.

void protocols::canonical_sampling::TrajectoryRecorder::reset	(	protocols::moves::MonteCarlo const &	mc,
		MetropolisHastingsMoverCAP	metropolis_hastings_mover = `0`
	)

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(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), 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,
		MetropolisHastingsMoverCAP	metropolis_hastings_mover = `0`
	)

Save the given pose to the trajectory.

I suspect this method is provided so that the trajectory classes can be used outside the canonical_sampling namespace. That explains why it's public, when it doesn't do anything but provide a simpler way for children to respond to observe_after_metropolis(). It also explains why it has so many different signatures and default arguments. Note that this function expects a MetropolisHastingsMoverCAP instead of the more usual MetropolisHastingsMover const &. This is because only pointers are compatible with null default arguments.

That said, it seems to me that the metropolis_hastings_mover argument is basically useless because you can't ever be sure it'll actually be provided. It's also surprising that observe_after_metropolis() is still virtual, because I would think that this method should supersede it.

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 )

Save the given pose to the trajectory.

I suspect this method is provided so that the trajectory classes can be used outside the canonical_sampling namespace. That explains why it's public, when it doesn't do anything but provide a simpler way for children to respond to observe_after_metropolis(). It also explains why it has so many different signatures and default arguments. Note that this function expects a MetropolisHastingsMoverCAP instead of the more usual MetropolisHastingsMover const &. This is because only pointers are compatible with null default arguments.

That said, it seems to me that the metropolis_hastings_mover argument is basically useless because you can't ever be sure it'll actually be provided. It's also surprising that observe_after_metropolis() is still virtual, because I would think that this method should supersede it.

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

virtual void protocols::canonical_sampling::TrajectoryRecorder::write_model	(	core::pose::Pose const &	pose,
		MetropolisHastingsMoverCAP	metropolis_hastings_mover = `0`
	)