#include <MetricRecorder.hh>

Inheritance diagram for protocols::canonical_sampling::MetricRecorder:

Collaboration diagram for protocols::canonical_sampling::MetricRecorder:

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

	~MetricRecorder ()
	Destructor. More...

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

MetricRecorder &	operator= (MetricRecorder const &)
	operator= More...

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual protocols::moves::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...

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...

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...

std::string const &	file_name () const

void	file_name (std::string const &file_name)

core::Size	stride () const

void	stride (core::Size stride)

bool	cumulate_jobs () const

void	cumulate_jobs (bool cumulate_jobs)

bool	cumulate_replicas () const

void	cumulate_replicas (bool cumulate_replicas)

bool	prepend_output_name () const

void	prepend_output_name (bool prepend_output_name)

void	add_torsion (core::id::TorsionID const &torsion_id, std::string name="")

void	add_torsion (core::pose::Pose const &pose, std::string const &rsd, std::string type, core::Size torsion, std::string name="")

void	reset (core::pose::Pose const &pose, 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)

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...

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

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_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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	write_model (core::pose::Pose const &pose)

Private Attributes
std::string	file_name_

core::Size	stride_

bool	cumulate_jobs_

bool	cumulate_replicas_

bool	prepend_output_name_

core::Size	step_count_

utility::io::ozstream	recorder_stream_

utility::vector1< std::pair < core::id::TorsionID, std::string > >	torsion_ids_

time_t	last_flush_

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

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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

Definition at line 54 of file MetricRecorder.hh.

Constructor & Destructor Documentation

protocols::canonical_sampling::MetricRecorder::MetricRecorder ( )

Constructor.

Definition at line 70 of file MetricRecorder.cc.

Referenced by fresh_instance().

protocols::canonical_sampling::MetricRecorder::~MetricRecorder ( )

Destructor.

Definition at line 79 of file MetricRecorder.cc.

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

Copy constructor.

Definition at line 82 of file MetricRecorder.cc.

Member Function Documentation

void protocols::canonical_sampling::MetricRecorder::add_torsion	(	core::id::TorsionID const &	torsion_id,
		std::string	name = `""`
	)

Definition at line 232 of file MetricRecorder.cc.

References torsion_ids_, and core::id::TorsionID::valid().

Referenced by add_torsion(), and parse_my_tag().

void protocols::canonical_sampling::MetricRecorder::add_torsion	(	core::pose::Pose const &	pose,
		std::string const &	rsd,
		std::string	type,
		core::Size	torsion,
		std::string	name = `""`
	)

Definition at line 250 of file MetricRecorder.cc.

References add_torsion(), core::id::BB, core::id::CHI, core::id::JUMP, and core::pose::parse_resnum().

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

virtual

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Definition at line 360 of file MetricRecorder.cc.

References update_after_boltzmann().

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

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 105 of file MetricRecorder.cc.

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

Definition at line 190 of file MetricRecorder.cc.

References cumulate_jobs_.

Referenced by cumulate_jobs().

void protocols::canonical_sampling::MetricRecorder::cumulate_jobs ( bool cumulate_jobs)

Definition at line 196 of file MetricRecorder.cc.

References cumulate_jobs(), and cumulate_jobs_.

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

Definition at line 204 of file MetricRecorder.cc.

References cumulate_replicas_.

Referenced by cumulate_replicas().

void protocols::canonical_sampling::MetricRecorder::cumulate_replicas ( bool cumulate_replicas)

Definition at line 210 of file MetricRecorder.cc.

References cumulate_replicas(), and cumulate_replicas_.

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

Definition at line 162 of file MetricRecorder.cc.

References file_name_.

Referenced by file_name(), and initialize_simulation().

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

Definition at line 168 of file MetricRecorder.cc.

References file_name(), and file_name_.

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

virtual

callback executed after all Monte Carlo trials

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Definition at line 398 of file MetricRecorder.cc.

References recorder_stream_.

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

virtual

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).

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.

Definition at line 111 of file MetricRecorder.cc.

References MetricRecorder().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 117 of file MetricRecorder.cc.

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

virtual

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

Definition at line 368 of file MetricRecorder.cc.

References cumulate_jobs_, cumulate_replicas_, file_name(), protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo(), protocols::canonical_sampling::MetropolisHastingsMover::output_file_name(), and reset().

void protocols::canonical_sampling::MetricRecorder::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.

Definition at line 387 of file MetricRecorder.cc.

References protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo(), and update_after_boltzmann().

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

operator=

Definition at line 97 of file MetricRecorder.cc.

void protocols::canonical_sampling::MetricRecorder::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.

Definition at line 123 of file MetricRecorder.cc.

References add_torsion(), cumulate_jobs_, cumulate_replicas_, file_name_, protocols::moves::Mover::name(), prepend_output_name_, stride_, and protocols::moves::Mover::type().

bool protocols::canonical_sampling::MetricRecorder::prepend_output_name ( ) const

Definition at line 218 of file MetricRecorder.cc.

References prepend_output_name_.

Referenced by prepend_output_name().

void protocols::canonical_sampling::MetricRecorder::prepend_output_name ( bool prepend_output_name)

Definition at line 224 of file MetricRecorder.cc.

References prepend_output_name(), and prepend_output_name_.

virtual bool protocols::canonical_sampling::MetricRecorder::reinitialize_for_each_job ( ) const

inlinevirtual

this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

Definition at line 133 of file MetricRecorder.hh.

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

Definition at line 278 of file MetricRecorder.cc.

References recorder_stream_, step_count_, and update_after_boltzmann().

Referenced by initialize_simulation().

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

Definition at line 176 of file MetricRecorder.cc.

References stride_.

Referenced by stride().

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

Definition at line 182 of file MetricRecorder.cc.

References stride(), and stride_.

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