Record a trajectory to an SQL database. More...

#include <DbTrajectoryRecorder.hh>

Classes
struct	Frame
	Helper struct used store cached poses. More...

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

	DbTrajectoryRecorder (core::Size job_id)
	Constructor with a job_id parameter to use as a foreign key. More...

	DbTrajectoryRecorder (core::Size job_id, core::Size temp_level)
	Constructor with job_id and temp_level parameters. More...

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

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

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

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

core::Size	job_id () const
	Return the job id that will be used as a foreign key in the trajectory table that gets generated. More...

void	set_job_id (core::Size id)
	Set the job id that will be used as a foreign key in the trajectory table that gets generated. More...

core::Size	temp_level () const
	Return the temperature level that this observer is focusing on. More...

void	set_temp_level (core::Size level)
	Set the temperature level that this observer should focus on. More...

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

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

bool	restart_simulation (core::pose::Pose &pose, MetropolisHastingsMover &mover, core::Size &cycle, core::Size &temp_level, core::Real &temperature)
	Not implemented, except to complain if accidentally used. More...

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

	~TrajectoryRecorder ()
	Destructor. More...

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

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 Member Functions
void	write_schema_to_db () const
	Generate the table schemas and write them to the database. More...

void	write_cache_to_db () const
	Write any cached poses into the database, then clear the cache. More...

void	write_model (core::pose::Pose const &pose, MetropolisHastingsMoverCAP mover=0)
	Append the given model to the trajectory being written. More...

void	write_first_model (core::pose::Pose const &pose, MetropolisHastingsMoverCAP mover)
	Write the starting structure to the database. More...

Private Attributes
core::Size	job_id_

core::Size	temp_level_

utility::vector1< Frame >	frame_cache_

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::canonical_sampling::TrajectoryRecorder
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 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

Record a trajectory to an SQL database.

This class builds upon Rosetta's database framework, which means that there is support for SQLite3, MySQL and PostgreSQL. Database options must be specified on the command line (i.e. there's no API for this):

# SQLite3
-out:use_database
-inout:dbms:database_name traj.sqlite
# MySQL
-out:use_database
-inout:dbms:mode mysql
-inout:dbms:database_name ...
-inout:dbms:user ...
-inout:dbms:port ...
-inout:dbms:password ...

Constructor & Destructor Documentation

protocols::canonical_sampling::DbTrajectoryRecorder::DbTrajectoryRecorder ( )

Default constructor.

Referenced by clone(), and fresh_instance().

protocols::canonical_sampling::DbTrajectoryRecorder::DbTrajectoryRecorder ( core::Size job_id )

Constructor with a job_id parameter to use as a foreign key.

protocols::canonical_sampling::DbTrajectoryRecorder::DbTrajectoryRecorder	(	core::Size	job_id,
		core::Size	temp_level
	)

Constructor with job_id and temp_level parameters.

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

Copy constructor.

Member Function Documentation

MoverOP protocols::canonical_sampling::DbTrajectoryRecorder::clone ( ) const

virtual

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.

References DbTrajectoryRecorder().

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

virtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation(), and write_cache_to_db().

MoverOP protocols::canonical_sampling::DbTrajectoryRecorder::fresh_instance ( ) const

virtual

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.

References DbTrajectoryRecorder().

string protocols::canonical_sampling::DbTrajectoryRecorder::get_name ( ) const

virtual

Return the name of this mover.

Reimplemented from protocols::canonical_sampling::TrajectoryRecorder.

void protocols::canonical_sampling::DbTrajectoryRecorder::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::TrajectoryRecorder.

References protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation(), write_first_model(), and write_schema_to_db().

core::Size protocols::canonical_sampling::DbTrajectoryRecorder::job_id ( ) const

inline

Return the job id that will be used as a foreign key in the trajectory table that gets generated.

References job_id_.

Referenced by write_schema_to_db().

bool protocols::canonical_sampling::DbTrajectoryRecorder::restart_simulation	(	core::pose::Pose &	pose,
		MetropolisHastingsMover &	mover,
		core::Size &	cycle,
		core::Size &	temp_level,
		core::Real &	temperature
	)

virtual

Not implemented, except to complain if accidentally used.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References utility_exit_with_message.

void protocols::canonical_sampling::DbTrajectoryRecorder::set_job_id ( core::Size id )

inline

Set the job id that will be used as a foreign key in the trajectory table that gets generated.

References job_id_.

void protocols::canonical_sampling::DbTrajectoryRecorder::set_temp_level ( core::Size level )

inline

Set the temperature level that this observer should focus on.

Temperature levels start counting from one. If zero is given, it will be taken to mean that every level should be recorded.

References temp_level_.

core::Size protocols::canonical_sampling::DbTrajectoryRecorder::temp_level ( ) const

inline

Return the temperature level that this observer is focusing on.

References temp_level_.

Referenced by write_cache_to_db(), write_model(), and write_schema_to_db().

void protocols::canonical_sampling::DbTrajectoryRecorder::write_cache_to_db ( ) const

private

Write any cached poses into the database, then clear the cache.

References core::io::silent::SilentFileData::_write_silent_struct(), basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), core::pose::Pose::energies(), frame(), frame_cache_, basic::database::get_db_session(), protocols::canonical_sampling::DbTrajectoryRecorder::Frame::iteration, job_id_, make_vector(), protocols::canonical_sampling::DbTrajectoryRecorder::Frame::pose, score, temp_level(), protocols::canonical_sampling::DbTrajectoryRecorder::Frame::temp_level, core::scoring::Energies::total_energy(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database().

Referenced by finalize_simulation(), and write_model().

void protocols::canonical_sampling::DbTrajectoryRecorder::write_first_model	(	core::pose::Pose const &	pose,
		MetropolisHastingsMoverCAP	mover
	)

private

Write the starting structure to the database.

This case is handled specially to guarantee that the frame labeled as "iteration 0" always represents the starting structure. In the future, this method will make sure only the root node writes this frame.

References frame(), frame_cache_, protocols::canonical_sampling::DbTrajectoryRecorder::Frame::iteration, protocols::canonical_sampling::DbTrajectoryRecorder::Frame::pose, and protocols::canonical_sampling::DbTrajectoryRecorder::Frame::temp_level.

Referenced by initialize_simulation().