#include <RationalMonteCarlo.hh>

Inheritance diagram for protocols::simple_moves::rational_mc::RationalMonteCarlo:

Collaboration diagram for protocols::simple_moves::rational_mc::RationalMonteCarlo:

Public Member Functions
	RationalMonteCarlo (moves::MoverOP mover, ScoreFunctionOP score, core::Size num_trials, core::Real temperature, bool recover_low)

void	apply (Pose &pose)
	Applies the underlying mover to <pose> the specified number of times. More...

std::string	get_name () const
	Returns this mover's name. More...

bool	recover_low () const

moves::MoverOP	mover () const

core::Size	num_trials () const

core::Real	temperature () const

const core::scoring::ScoreFunction &	score_function () const

void	reset (const core::pose::Pose &pose)
	Updates the last accepted and lowest scoring pose members of the MonteCarlo member variable to the score of the specified pose. More...

const core::pose::Pose &	lowest_score_pose () const

const core::pose::Pose &	last_accepted_pose () const

void	set_mover (moves::MoverOP mover)

void	set_recover_low (bool recover_low)

void	set_num_trials (core::Size num_trials)

void	set_temperature (core::Real temperature)

void	enable_autotemp (core::Real quench)

void	disable_autotemp ()

void	set_score_function (core::scoring::ScoreFunctionOP score)
	Updates the score function. Before calling this method, make sure that apply() has been called at least once on a non-empty pose. More...

core::Size	add_trigger (const RationalMonteCarloTrigger &trigger)
	Registers the specified trigger with this instance. Returns a unique identifier for referring to this trigger in subsequent operations. More...

void	remove_trigger (core::Size trigger_id)
	Unregisters the trigger with the given unique identifier. 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...

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

Protected Member Functions
void	fire_all_triggers (const Pose &pose)
	Executes all triggers attached to this instance. The order of trigger execution is undefined. Do not assume, depend, or in any way rely upon a partiular ordering. 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...

Private Types
typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

Private Attributes
moves::MoverOP	mover_
	Underlying mover. More...

moves::MonteCarloOP	mc_
	Determines whether applications of the base mover should be accepted by applying the Metropolis criterion to the pose. More...

core::Size	num_trials_
	Number of times to execute the underlying mover in calls to apply() More...

bool	recover_low_
	Determines whether the low scoring pose should be recovered at the conclusion of the apply() method. More...

Triggers	triggers_
	Collection of function callbacks. More...

core::Size	next_trigger_id_
	Next trigger id to be assigned. More...

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...

Detailed Description

Definition at line 45 of file RationalMonteCarlo.hh.

Member Typedef Documentation

typedef core::pose::Pose protocols::simple_moves::rational_mc::RationalMonteCarlo::Pose

private

Definition at line 46 of file RationalMonteCarlo.hh.

typedef core::scoring::ScoreFunctionOP protocols::simple_moves::rational_mc::RationalMonteCarlo::ScoreFunctionOP

private

Definition at line 47 of file RationalMonteCarlo.hh.

Constructor & Destructor Documentation

protocols::simple_moves::rational_mc::RationalMonteCarlo::RationalMonteCarlo	(	moves::MoverOP	mover,
		ScoreFunctionOP	score,
		core::Size	num_trials,
		core::Real	temperature,
		bool	recover_low
	)

Definition at line 51 of file RationalMonteCarlo.cc.

References protocols::viewer::add_monte_carlo_viewer(), and mc_.

Member Function Documentation

Size protocols::simple_moves::rational_mc::RationalMonteCarlo::add_trigger ( const RationalMonteCarloTrigger & trigger)

Registers the specified trigger with this instance. Returns a unique identifier for referring to this trigger in subsequent operations.

Definition at line 85 of file RationalMonteCarlo.cc.

References next_trigger_id_, and triggers_.

void protocols::simple_moves::rational_mc::RationalMonteCarlo::apply ( Pose & pose)

virtual

Applies the underlying mover to <pose> the specified number of times.

Implements protocols::moves::Mover.

Definition at line 57 of file RationalMonteCarlo.cc.

References fire_all_triggers(), mc_, mover_, num_trials(), and recover_low().

Referenced by protocols::star::StarAbinitio::apply().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::disable_autotemp ( )

Definition at line 165 of file RationalMonteCarlo.cc.

References mc_.

void protocols::simple_moves::rational_mc::RationalMonteCarlo::enable_autotemp ( core::Real quench)

Definition at line 161 of file RationalMonteCarlo.cc.

References mc_.

Referenced by protocols::star::StarAbinitio::apply().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::fire_all_triggers ( const Pose & pose)

protected

Executes all triggers attached to this instance. The order of trigger execution is undefined. Do not assume, depend, or in any way rely upon a partiular ordering.

Definition at line 100 of file RationalMonteCarlo.cc.

References core::scoring::hbonds::t(), and triggers_.

Referenced by apply().

std::string protocols::simple_moves::rational_mc::RationalMonteCarlo::get_name ( ) const

virtual

Returns this mover's name.

Implements protocols::moves::Mover.

Definition at line 81 of file RationalMonteCarlo.cc.

const Pose & protocols::simple_moves::rational_mc::RationalMonteCarlo::last_accepted_pose ( ) const

Definition at line 132 of file RationalMonteCarlo.cc.

References mc_.

const Pose & protocols::simple_moves::rational_mc::RationalMonteCarlo::lowest_score_pose ( ) const

Definition at line 128 of file RationalMonteCarlo.cc.

References mc_.

MoverOP protocols::simple_moves::rational_mc::RationalMonteCarlo::mover ( ) const

Definition at line 116 of file RationalMonteCarlo.cc.

References mover_.

Referenced by set_mover().

Size protocols::simple_moves::rational_mc::RationalMonteCarlo::num_trials ( ) const

Definition at line 108 of file RationalMonteCarlo.cc.

References num_trials_.

Referenced by apply(), and set_num_trials().

bool protocols::simple_moves::rational_mc::RationalMonteCarlo::recover_low ( ) const

Definition at line 112 of file RationalMonteCarlo.cc.

References recover_low_.

Referenced by apply(), and set_recover_low().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::remove_trigger ( core::Size trigger_id)

Unregisters the trigger with the given unique identifier.

Definition at line 91 of file RationalMonteCarlo.cc.

References triggers_.

void protocols::simple_moves::rational_mc::RationalMonteCarlo::reset ( const core::pose::Pose & pose)

Updates the last accepted and lowest scoring pose members of the MonteCarlo member variable to the score of the specified pose.

Definition at line 157 of file RationalMonteCarlo.cc.

References mc_.

const ScoreFunction & protocols::simple_moves::rational_mc::RationalMonteCarlo::score_function ( ) const

Definition at line 124 of file RationalMonteCarlo.cc.

References mc_.

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_mover ( moves::MoverOP mover)

Definition at line 145 of file RationalMonteCarlo.cc.

References mover(), and mover_.

Referenced by protocols::star::configure_rmc().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_num_trials ( core::Size num_trials)

Definition at line 137 of file RationalMonteCarlo.cc.

References num_trials(), and num_trials_.

Referenced by protocols::star::configure_rmc().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_recover_low ( bool recover_low)

Definition at line 141 of file RationalMonteCarlo.cc.

References recover_low(), and recover_low_.

Referenced by protocols::star::configure_rmc().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_score_function ( core::scoring::ScoreFunctionOP score)

Updates the score function. Before calling this method, make sure that apply() has been called at least once on a non-empty pose.

Definition at line 153 of file RationalMonteCarlo.cc.

References mc_.

Referenced by protocols::star::configure_rmc().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_temperature ( core::Real temperature)

Definition at line 149 of file RationalMonteCarlo.cc.

References mc_.

Referenced by protocols::star::configure_rmc().

Real protocols::simple_moves::rational_mc::RationalMonteCarlo::temperature ( ) const

Definition at line 120 of file RationalMonteCarlo.cc.

References mc_.

Member Data Documentation

moves::MonteCarloOP protocols::simple_moves::rational_mc::RationalMonteCarlo::mc_

private

Determines whether applications of the base mover should be accepted by applying the Metropolis criterion to the pose.

Definition at line 109 of file RationalMonteCarlo.hh.

Referenced by apply(), disable_autotemp(), enable_autotemp(), last_accepted_pose(), lowest_score_pose(), RationalMonteCarlo(), reset(), score_function(), set_score_function(), set_temperature(), and temperature().

moves::MoverOP protocols::simple_moves::rational_mc::RationalMonteCarlo::mover_

private

Underlying mover.

Definition at line 105 of file RationalMonteCarlo.hh.

Referenced by apply(), mover(), and set_mover().

core::Size protocols::simple_moves::rational_mc::RationalMonteCarlo::next_trigger_id_

private

Next trigger id to be assigned.

Definition at line 122 of file RationalMonteCarlo.hh.

Referenced by add_trigger().

core::Size protocols::simple_moves::rational_mc::RationalMonteCarlo::num_trials_

private

Number of times to execute the underlying mover in calls to apply()

Definition at line 112 of file RationalMonteCarlo.hh.

Referenced by num_trials(), and set_num_trials().

bool protocols::simple_moves::rational_mc::RationalMonteCarlo::recover_low_

private

Determines whether the low scoring pose should be recovered at the conclusion of the apply() method.

Definition at line 116 of file RationalMonteCarlo.hh.

Referenced by recover_low(), and set_recover_low().

Triggers protocols::simple_moves::rational_mc::RationalMonteCarlo::triggers_

private

Collection of function callbacks.

Definition at line 119 of file RationalMonteCarlo.hh.

Referenced by add_trigger(), fire_all_triggers(), and remove_trigger().

The documentation for this class was generated from the following files:

src/protocols/simple_moves/rational_mc/RationalMonteCarlo.hh
src/protocols/simple_moves/rational_mc/RationalMonteCarlo.cc

Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation