Run a sidechain-only canonical Monte Carlo simulation. More...

#include <SidechainMetropolisHastingsMover.hh>

Inheritance diagram for protocols::canonical_sampling::SidechainMetropolisHastingsMover:

Public Types
typedef MetropolisHastingsMover	Parent

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

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

	SidechainMetropolisHastingsMover (core::Size stride)
	Constructor with stride parameter. More...

	SidechainMetropolisHastingsMover (SidechainMetropolisHastingsMover const &metropolis_hastings_mover)
	Copy constructor. More...

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

void	apply (core::pose::Pose &pose) override
	Run the sidechain-only simulation. 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 the name of this mover. More...

protocols::moves::MoverOP	fresh_instance () const override
	Return a newly instantiated mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Use a RosettaScripts tag to configure this mover. More...

bool	pass_metropolis (core::Real delta_energy, core::Real last_proposal_density_ratio) const
	Return true if a move should be accepted, given delta_energy and proposal_density_ratio. More...

core::Size	output_count (core::Size ct) const
	Return non-zero if the observers should be invoked on this iteration. More...

void	set_stride (core::Size setting)
	Set the frequency with which the observers should be invoked. More...

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

	MetropolisHastingsMover (MetropolisHastingsMover const &metropolis_hastings_mover)
	Copy constructor. More...

	~MetropolisHastingsMover () override
	Destructor. More...

bool	reinitialize_for_each_job () const override
	Return false. This mover does not need to be reinitialized for each job. More...

bool	reinitialize_for_new_input () const override
	Return false. This mover does not need to be reinitialized for new input. More...

protocols::moves::MonteCarloCOP	monte_carlo () const
	Return the MonteCarlo object being used by this simulation. More...

void	set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo)
	Provide a MonteCarlo object to use for this simulation. More...

TemperatureControllerCOP	tempering () const
	Return the TemperatureController being used by this simulation. More...

void	set_tempering (TemperatureControllerOP)
	Provide a TemperatureController to use for this simulation. More...

core::Size	ntrials () const
	Return the number of iterations used by this simulation. More...

void	set_ntrials (core::Size ntrials)
	Set the number of iterations to use for this simulation. More...

core::Size	current_trial () const
	Return the iteration currently being processed by the simulation. More...

std::string const &	output_name () const
	Return the file name used by some of the observers to output data. More...

void	set_output_name (std::string const &output_name)
	Set the file name used by some of the observers to output data. More...

std::string	output_file_name (std::string const &suffix, bool cumulate_jobs=false, bool cumulate_replicas=false) const
	Return a file name that is consistent with the given options. More...

virtual ThermodynamicMoverOP	random_mover () const
	Return true if the simulation has been completed. More...

virtual void	add_mover (ThermodynamicMoverOP mover, core::Real weight, utility::tag::TagCOP const &subtag)
	Add the given mover to the simulation. More...

virtual void	add_mover (ThermodynamicMoverOP mover, core::Real weight)
	Add the given mover to the simulation. More...

void	add_backrub_mover (core::Real weight)
	Convenience method to add a backrub move to the simulation. More...

void	add_kic_mover (core::Real weight, protocols::loops::Loop const &loop)
	Convenience method to add a kinematic closure move to the simulation. More...

void	add_small_mover (core::Real weight)
	Convenience method to add a small move to the simulation. More...

void	add_shear_mover (core::Real weight)
	Convenience method to add a shear move to the simulation. More...

void	add_sidechain_mover (core::Real weight, core::Real prob_uniform, core::Real prob_withinrot, bool preserve_cbeta)
	Convenience method to add a sidechain move to the simulation. More...

void	add_sidechain_mc_mover (core::Real weight, core::Real prob_uniform, core::Real prob_withinrot, bool preserve_cbeta, core::Size ntrials)
	Convenience method to add a Monte Carlo sidechain move to the simulation. This move uses an internal Monte Carlo loop to generate a whole new set of sidechain conformations. More...

void	add_observer (ThermodynamicObserverOP observer)
	Add the given observer to this simulation. More...

ThermodynamicMover const &	last_move () const
	Return the most recently used ThermodynamicMover. More...

bool	last_accepted () const
	Return true if the last attempted move was accepted. More...

std::string	get_last_checkpoint () const

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...

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes
core::Size	stride_

Additional Inherited Members
Static Public Member Functions inherited from protocols::canonical_sampling::MetropolisHastingsMover
static std::string	mover_name ()

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

static std::string	mover_or_add_group_name ()

static std::string	add_ct_name (std::string)

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::canonical_sampling::MetropolisHastingsMover
TemperatureControllerOP const &	tempering ()
	Protected non-const access to the TemperatureController. More...

ThermodynamicMoverOP	mover_by_index (numeric::Size idx) const
	Return the mover that was added at the given index. More...

void	write_checkpoint (core::pose::Pose const &pose)
	write checkpoint snapshots for restarting More...

bool	get_checkpoints ()
	get checkpoint_id for restarting More...

void	wind_down_simulation (core::pose::Pose &pose)
	Finalize all the movers and observers used in this simulation, and write some debrief statistics to the tracer. More...

core::Size	prepare_simulation (core::pose::Pose &pose)
	Initialize all the movers and observers to be used in this simulation. More...

void	set_last_accepted (bool setting)
	Indicate whether or not the last attempted move was accepted. More...

void	set_last_move (ThermodynamicMoverOP setting)
	Indicate what type of move was last attempted. More...

utility::vector1 < ThermodynamicObserverOP > const &	observers ()
	Return a list of all observers attached to this simulation. More...

protocols::moves::MonteCarlo &	nonconst_monte_carlo ()
	Protected non-const access to the MonteCarlo object. 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

Run a sidechain-only canonical Monte Carlo simulation.

The Monte Carlo algorithm present in apply() has been optimized for the case where only the sidechains can moves. This makes it possible speed up score function evaluation by either precalculating and/or caching residue pair energies. In this specific case, however, I'm not exactly sure how the algorithm is doing its optimization.

Warning: Although this class inherits from MetropolisHastingsMover, it doesn't support all of its parent's interface. In particular, since the algorithm is customized for a particular sidechain move, movers added via add_mover() or its related methods are ignored. However, observers added via add_observer() can still be used to report on the state of the simulation.

Member Typedef Documentation

typedef MetropolisHastingsMover protocols::canonical_sampling::SidechainMetropolisHastingsMover::Parent

Constructor & Destructor Documentation

protocols::canonical_sampling::SidechainMetropolisHastingsMover::SidechainMetropolisHastingsMover ( )

Default constructor.

protocols::canonical_sampling::SidechainMetropolisHastingsMover::SidechainMetropolisHastingsMover ( core::Size stride )

Constructor with stride parameter.

protocols::canonical_sampling::SidechainMetropolisHastingsMover::SidechainMetropolisHastingsMover ( SidechainMetropolisHastingsMover const & metropolis_hastings_mover )

default

Copy constructor.

protocols::canonical_sampling::SidechainMetropolisHastingsMover::~SidechainMetropolisHastingsMover ( )

overridedefault

Default destructor.

Member Function Documentation

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

overridevirtual

Run the sidechain-only simulation.

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

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

overridevirtual

Return the name of this mover.

Return a copy of this mover.

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

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

overridevirtual

Return a newly instantiated mover.

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

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

overridevirtual

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

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

core::Size protocols::canonical_sampling::SidechainMetropolisHastingsMover::output_count ( core::Size ct ) const

Return non-zero if the observers should be invoked on this iteration.

See also: set_stride()

References stride_.

Referenced by apply().

void protocols::canonical_sampling::SidechainMetropolisHastingsMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Use a RosettaScripts tag to configure this mover.

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

References protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), and stride_.

bool protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis	(	core::Real	delta_energy,
		core::Real	last_proposal_density_ratio
	)		const