A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object. More...

#include <TrialMover.hh>

Inheritance diagram for protocols::moves::TrialMover:

Public Types
typedef core::Real	Real

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

Public Member Functions
	TrialMover ()

	TrialMover (MoverOP mover_in, MonteCarloOP mc_in)
	Constructs a TrialMover trialmover = TrialMover( mover_in , mc_in ) More...

	TrialMover (TrialMover const &object_to_copy)
	Copy constructor. More...

	~TrialMover () override

virtual void	initialize_weights (Real const start_weight, Real const end_weight, core::scoring::ScoreType score_type, int const ramp_cycles)

void	apply (core::pose::Pose &pose) override
	Performs a single trial, apply the Mover and accept or reject the move based on the MonteCarlo acceptance criteria. More...

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

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

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

Real	acceptance_rate () const

int	num_accepts () const
	Returns the number of moves accepted by this TrialMover. More...

void	set_mc (MonteCarloOP mc_in)
	Sets the MonteCarlo object to <mc_in> More...

MoverOP	mover () const
	Returns the underlying Mover. More...

MonteCarlo const &	mc () const
	Returns the underlying MonteCarlo object. More...

StatsType	keep_stats_type () const

void	keep_stats_type (StatsType setting)

void	set_input_pose (PoseCOP pose) override
	setter for poses contained for rms More...

void	set_native_pose (PoseCOP pose) override
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &) override
	Requires that a MonteCarlo object has already been loaded into the basic::datacache::DataMap in a prior MONTECARLOS objects section. 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...

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...

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...

Protected Attributes
MoverOP	mover_

MonteCarloOP	mc_

MoverStatistics	stats_

Private Attributes
Real	start_weight_

Real	original_weight

Real	ramp_weight

Real	delta

StatsType	stats_type_

Friends
std::ostream &	operator<< (std::ostream &os, TrialMover const &mover)

Additional Inherited Members
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

A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object.

Common Methods: TrialMover.apply TrialMover.set_mc

Member Typedef Documentation

typedef core::Real protocols::moves::TrialMover::Real

Constructor & Destructor Documentation

protocols::moves::TrialMover::TrialMover ( )

protocols::moves::TrialMover::TrialMover	(	MoverOP	mover_in,
		MonteCarloOP	mc_in
	)

Constructs a TrialMover trialmover = TrialMover( mover_in , mc_in )

Mover mover_in /object defining what move to make MonteCarlo mc_in /object defining acceptance

References mc_, and mover_.

protocols::moves::TrialMover::TrialMover ( TrialMover const & object_to_copy )

Copy constructor.

protocols::moves::TrialMover::~TrialMover ( )

overridedefault

Member Function Documentation

Real protocols::moves::TrialMover::acceptance_rate ( ) const

References protocols::moves::MoverStatistics::acceptance_rate(), stats_, and protocols::moves::tr().

void protocols::moves::TrialMover::apply ( core::pose::Pose & pose )

overridevirtual

Performs a single trial, apply the Mover and accept or reject the move based on the MonteCarlo acceptance criteria.

: the apply function for a trial

example(s): trialmover.apply(pose) See Also: Pose MonteCarlo MonteCarlo.boltzmann RepeatMover SequenceMover TrialMover

: the trial object is created with an mc object the mover is applied before doing an mc.boltzmann

Author: : Monica Berrondo

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_filters::EvaluatedTrialMover.

References protocols::moves::accept_reject, protocols::moves::MoverStatistics::accepted(), protocols::moves::MoverStatistics::add_score(), protocols::moves::all_stats, core::pose::Pose::energies(), keep_stats_type(), mc_, mover_, protocols::moves::no_stats, protocols::moves::MoverStatistics::print(), stats_, stats_type_, core::scoring::Energies::total_energy(), and core::scoring::total_score.

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::do_frag_cycles().

protocols::moves::MoverOP protocols::moves::TrialMover::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.

protocols::moves::MoverOP protocols::moves::TrialMover::fresh_instance ( ) const

overridevirtual

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.

std::string protocols::moves::TrialMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_filters::EvaluatedTrialMover.

Referenced by protocols::moves::operator<<().

void protocols::moves::TrialMover::initialize_weights	(	Real const	start_weight,
		Real const	end_weight,
		core::scoring::ScoreType	score_type,
		int const	ramp_cycles
	)

virtual

References delta, mc_, original_weight, ramp_weight, and start_weight_.

StatsType protocols::moves::TrialMover::keep_stats_type ( ) const

inline

References stats_type_.

Referenced by protocols::simple_filters::EvaluatedTrialMover::apply(), and apply().

void protocols::moves::TrialMover::keep_stats_type ( StatsType setting )

inline

References stats_type_.

MonteCarlo const& protocols::moves::TrialMover::mc ( ) const

inline

Returns the underlying MonteCarlo object.

References mc_.

MoverOP protocols::moves::TrialMover::mover ( ) const

inline

Returns the underlying Mover.

References mover_.

Referenced by protocols::moves::operator<<().

int protocols::moves::TrialMover::num_accepts ( ) const

Returns the number of moves accepted by this TrialMover.

References protocols::moves::MoverStatistics::num_accepted(), and stats_.

Referenced by protocols::moves::operator<<().

void protocols::moves::TrialMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	filters,
		Movers_map const &	movers,
		Pose const &
	)