#include <TrajectoryRecorder.hh>

Inheritance diagram for protocols::canonical_sampling::TrajectoryRecorder:

Collaboration diagram for protocols::canonical_sampling::TrajectoryRecorder:

Public Member Functions
	TrajectoryRecorder ()
	Constructor. More...

	~TrajectoryRecorder ()
	Destructor. More...

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

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

virtual void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string const &	file_name () const

void	file_name (std::string const &file_name)

core::Size	model_count () const

core::Size	step_count () const

core::Size	stride () const

bool	cumulate_jobs () const

bool	cumulate_replicas () const

void	stride (core::Size stride)

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

void	update_after_boltzmann (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMoverCAP metropolis_hastings_mover=0)

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

virtual void	apply (core::pose::Pose &pose)

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

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

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicObserver
	ThermodynamicObserver ()

virtual	~ThermodynamicObserver ()

virtual bool	restart_simulation (core::pose::Pose &, protocols::canonical_sampling::MetropolisHastingsMover &, core::Size &, core::Size &, core::Real &)
	callback executed before any Monte Carlo trials More...

virtual void	finalize_simulation (core::pose::Pose &, protocols::canonical_sampling::MetropolisHastingsMover const &)
	callback executed after all Monte Carlo trials More...

virtual bool	requires_pose ()
	return false here if a valid pose is not required for "observe" i.e. a trialcounter 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
	clone has to be overridden only if clone invocation is expected. 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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

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

Protected Member Functions
virtual void	write_model (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMoverCAP metropolis_hastings_mover=0)=0

Private Member Functions
TrajectoryRecorder &	operator= (TrajectoryRecorder const &)

Private Attributes
core::Size	stride_

core::Size	model_count_

core::Size	step_count_

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::TagPtr	TagPtr

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

Definition at line 45 of file TrajectoryRecorder.hh.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 61 of file TrajectoryRecorder.cc.

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

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

Destructor.

Definition at line 78 of file TrajectoryRecorder.cc.

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

Copy constructor.

Definition at line 81 of file TrajectoryRecorder.cc.

Member Function Documentation

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

virtual

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Definition at line 150 of file TrajectoryRecorder.cc.

References update_after_boltzmann().

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

inline

Definition at line 95 of file TrajectoryRecorder.hh.

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

Definition at line 99 of file TrajectoryRecorder.hh.

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

Definition at line 75 of file TrajectoryRecorder.hh.

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

Definition at line 79 of file TrajectoryRecorder.hh.

References file_name(), and file_name_.

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

virtual

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

Implements protocols::moves::Mover.

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

Definition at line 102 of file TrajectoryRecorder.cc.

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

virtual

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Reimplemented in protocols::canonical_sampling::SilentTrajectoryRecorder.

Definition at line 155 of file TrajectoryRecorder.cc.

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

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

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

inline

Definition at line 83 of file TrajectoryRecorder.hh.

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)

virtual

callback executed after the Metropolis criterion is evaluated

Implements protocols::canonical_sampling::ThermodynamicObserver.

Reimplemented in protocols::canonical_sampling::SilentTrajectoryRecorder.

Definition at line 171 of file TrajectoryRecorder.cc.

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

Definition at line 94 of file TrajectoryRecorder.cc.

void protocols::canonical_sampling::TrajectoryRecorder::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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.

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

Definition at line 108 of file TrajectoryRecorder.cc.

References 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

Associates relevant options with the TemperedDocking class.

Definition at line 47 of file TrajectoryRecorder.cc.

References protocols::evaluation::options_registered_.

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

virtual

Reimplemented in protocols::canonical_sampling::PDBTrajectoryRecorder.

Definition at line 123 of file TrajectoryRecorder.cc.

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

Definition at line 87 of file TrajectoryRecorder.hh.

References step_count_.

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

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

inline

Definition at line 91 of file TrajectoryRecorder.hh.

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

Definition at line 103 of file TrajectoryRecorder.hh.

References stride(), and stride_.

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

Definition at line 132 of file TrajectoryRecorder.cc.

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)

Definition at line 145 of file TrajectoryRecorder.cc.

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::MetropolisHastingsMoverCAP	metropolis_hastings_mover = `0`
	)