Record the acceptance rate for every type of move attempted. More...

#include <TrialCounterObserver.hh>

Inheritance diagram for protocols::canonical_sampling::TrialCounterObserver:

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

	~TrialCounterObserver () override
	Default destructor. More...

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

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) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...

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

bool	requires_pose () override
	Return false, as a valid pose is not required for counting trials. More...

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

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

	~ThermodynamicObserver () override
	Destructor. More...

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

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 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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Attributes
protocols::canonical_sampling::MultiTemperatureTrialCounter	counters_

std::string	file_

core::Size	io_stride_

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

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 the acceptance rate for every type of move attempted.

Most of the work is done by observe_after_metropolis(). Separate statistics are recorded for moves made at different temperature levels.

Constructor & Destructor Documentation

protocols::canonical_sampling::TrialCounterObserver::TrialCounterObserver ( )

Default constructor.

protocols::canonical_sampling::TrialCounterObserver::~TrialCounterObserver ( )

overridedefault

Default destructor.

Member Function Documentation

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

overridevirtual

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.

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

overridevirtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References counters_, file_, protocols::canonical_sampling::MetropolisHastingsMover::output_name(), protocols::canonical_sampling::MultiTemperatureTrialCounter::show(), protocols::canonical_sampling::tr(), and protocols::canonical_sampling::MultiTemperatureTrialCounter::write_to_file().

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::canonical_sampling::TrialCounterObserver::initialize_simulation	(	core::pose::Pose &	,
		protocols::canonical_sampling::MetropolisHastingsMover const &	,
		core::Size
	)

overridevirtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References counters_, protocols::canonical_sampling::MultiTemperatureTrialCounter::reset(), protocols::canonical_sampling::MultiTemperatureTrialCounter::set_temperature_observer(), and protocols::canonical_sampling::MetropolisHastingsMover::tempering().

std::string protocols::canonical_sampling::TrialCounterObserver::mover_name ( )

static

Referenced by get_name(), protocols::canonical_sampling::TrialCounterObserverCreator::keyname(), and provide_xml_schema().

void protocols::canonical_sampling::TrialCounterObserver::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::MultiTemperatureTrialCounter::count_accepted(), protocols::canonical_sampling::MultiTemperatureTrialCounter::count_trial(), counters_, protocols::canonical_sampling::MetropolisHastingsMover::current_trial(), file_, io_stride_, protocols::canonical_sampling::MetropolisHastingsMover::last_accepted(), protocols::canonical_sampling::MetropolisHastingsMover::last_move(), protocols::canonical_sampling::MetropolisHastingsMover::output_name(), core::id::to_string(), protocols::moves::Mover::type(), and protocols::canonical_sampling::MultiTemperatureTrialCounter::write_to_file().

void protocols::canonical_sampling::TrialCounterObserver::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
	)

overridevirtual

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.

References file_, and io_stride_.

void protocols::canonical_sampling::TrialCounterObserver::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::canonical_sampling::TrialCounterObserverCreator::provide_xml_schema().

bool protocols::canonical_sampling::TrialCounterObserver::requires_pose ( )

inlineoverridevirtual

Return false, as a valid pose is not required for counting trials.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.