#include <BackrubSidechainMover.hh>

Inheritance diagram for protocols::backrub::BackrubSidechainMover:

Collaboration diagram for protocols::backrub::BackrubSidechainMover:

Public Member Functions
	BackrubSidechainMover ()

	BackrubSidechainMover (BackrubSidechainMover const &mover)

virtual	~BackrubSidechainMover ()

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...

void	update_segments (core::pose::Pose const &pose)

virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
	callback executed before any Monte Carlo trials More...

virtual void	apply (core::pose::Pose &pose)

virtual void	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	callback 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...

utility::vector1< core::Size > const &	pivot_residues () const

void	set_pivot_residues (utility::vector1< core::Size > const &pivot_residues)

core::pack::task::TaskFactoryCOP	task_factory () const

void	set_task_factory (core::pack::task::TaskFactoryOP task_factory)

core::Real	prob_uniform () const
	get the probability of uniformly sampling chi angles More...

void	set_prob_uniform (core::Real prob_uniform)
	set the probability of uniformly sampling chi angles More...

core::Real	prob_withinrot () const
	get the probability of sampling within the same rotamer More...

void	set_prob_withinrot (core::Real prob_withinrot)
	set the probability of sampling within the same rotamer More...

core::Real	prob_random_pert_current () const

void	set_prob_random_pert_current (core::Real prob_pert)

virtual bool	preserve_detailed_balance () const
	get whether detailed balance is preserved More...

virtual void	set_preserve_detailed_balance (bool preserve_detailed_balance)
	set whether detailed balance is preserved More...

bool	require_mm_bend () const
	get whether to exit during initialize_simulation if the mm_bend term isn't turned on More...

void	set_require_mm_bend (bool require_mm_bend)
	set whether to exit during initialize_simulation if the mm_bend term isn't turned on More...

virtual utility::vector1 < core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose)
	get the TorsionIDs perturbed by the mover during moves, along with their ranges More...

bool	record_statistics () const
	get whether to record mover statistics or not More...

void	set_record_statistics (bool record_statistics)
	set whether to record mover statistics or not More...

std::string const &	statistics_filename () const
	get filename for statistics output More...

void	set_statistics_filename (std::string const &statistics_filename)
	set filename for statistics output More...

void	reset_statistics ()

void	output_statistics (std::ostream &out)

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()

virtual	~ThermodynamicMover ()

virtual core::Real	last_proposal_density_ratio ()
	callback for proposal density ratio of last apply method More...

virtual bool	is_multi_trial ()
	determine whether the move performs multiple trials on a single apply More...

virtual core::Real	last_inner_score_temperature_delta ()
	get change in internal score/temperature for last apply method of multiple trial movers More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	get the MetropolisHastingsMover for multiple trial movers More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	set the MetropolisHastingsMover for multiple trial movers More...

virtual utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	get the DOF_IDs perturbed by the mover during moves (not including those returned by torsion_id_ranges(), along with their ranges 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...

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_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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	setup_histograms ()

void	record_histograms (bool accept)

void	update_type ()

Private Attributes
protocols::backrub::BackrubMoverOP	backrub_mover_

protocols::simple_moves::sidechain_moves::SidechainMoverOP	sidechain_mover_

utility::vector1< core::Size >	valid_segments_

core::Size	last_valid_segment_index_

core::Real	last_chi1_pre_

core::Real	last_chi1_post_

bool	record_statistics_

std::string	statistics_filename_

utility::vector1 < numeric::MultiDimensionalHistogram >	proposal_hists_

utility::vector1 < numeric::MultiDimensionalHistogram >	accept_hists_

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 44 of file BackrubSidechainMover.hh.

Constructor & Destructor Documentation

protocols::backrub::BackrubSidechainMover::BackrubSidechainMover ( )

Definition at line 87 of file BackrubSidechainMover.cc.

References backrub_mover_.

protocols::backrub::BackrubSidechainMover::BackrubSidechainMover ( BackrubSidechainMover const & mover)

Definition at line 99 of file BackrubSidechainMover.cc.

References backrub_mover_, and sidechain_mover_.

protocols::backrub::BackrubSidechainMover::~BackrubSidechainMover ( )

virtual

Definition at line 123 of file BackrubSidechainMover.cc.

Member Function Documentation

void protocols::backrub::BackrubSidechainMover::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 243 of file BackrubSidechainMover.cc.

References core::pose::Pose::chi(), core::pose::Pose::fold_tree(), and protocols::RG().

protocols::moves::MoverOP protocols::backrub::BackrubSidechainMover::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 126 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::finalize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover
	)

virtual

callback executed after all Monte Carlo trials

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Definition at line 277 of file BackrubSidechainMover.cc.

References protocols::abinitio::filename(), and protocols::canonical_sampling::MetropolisHastingsMover::output_name().

protocols::moves::MoverOP protocols::backrub::BackrubSidechainMover::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 132 of file BackrubSidechainMover.cc.

std::string protocols::backrub::BackrubSidechainMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 138 of file BackrubSidechainMover.cc.

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

virtual

callback executed before any Monte Carlo trials

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Definition at line 225 of file BackrubSidechainMover.cc.

References core::pose::Pose::fold_tree().

void protocols::backrub::BackrubSidechainMover::observe_after_metropolis ( protocols::canonical_sampling::MetropolisHastingsMover const & metropolis_hastings_mover)

virtual

callback after the Metropolis criterion is evaluated

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Definition at line 269 of file BackrubSidechainMover.cc.

References protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo().

void protocols::backrub::BackrubSidechainMover::output_statistics ( std::ostream & out)

Definition at line 441 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::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 144 of file BackrubSidechainMover.cc.

References core::sequence::end, protocols::moves::DataMap::get(), core::pose::get_resnum_list(), and protocols::moves::DataMap::has().

utility::vector1< core::Size > const & protocols::backrub::BackrubSidechainMover::pivot_residues ( ) const

Definition at line 297 of file BackrubSidechainMover.cc.

bool protocols::backrub::BackrubSidechainMover::preserve_detailed_balance ( ) const

virtual

get whether detailed balance is preserved

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 368 of file BackrubSidechainMover.cc.

core::Real protocols::backrub::BackrubSidechainMover::prob_random_pert_current ( ) const

Definition at line 354 of file BackrubSidechainMover.cc.

core::Real protocols::backrub::BackrubSidechainMover::prob_uniform ( ) const

get the probability of uniformly sampling chi angles

Definition at line 326 of file BackrubSidechainMover.cc.

core::Real protocols::backrub::BackrubSidechainMover::prob_withinrot ( ) const

get the probability of sampling within the same rotamer

Definition at line 340 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::record_histograms ( bool accept)

private

Definition at line 498 of file BackrubSidechainMover.cc.

bool protocols::backrub::BackrubSidechainMover::record_statistics ( ) const

get whether to record mover statistics or not

Definition at line 405 of file BackrubSidechainMover.cc.

bool protocols::backrub::BackrubSidechainMover::require_mm_bend ( ) const

get whether to exit during initialize_simulation if the mm_bend term isn't turned on

Definition at line 383 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::reset_statistics ( )

Definition at line 435 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_pivot_residues ( utility::vector1< core::Size > const & pivot_residues)

Definition at line 303 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_preserve_detailed_balance ( bool preserve_detailed_balance)

virtual

set whether detailed balance is preserved

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 374 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_prob_random_pert_current ( core::Real prob_pert)

Definition at line 360 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_prob_uniform ( core::Real prob_uniform)

set the probability of uniformly sampling chi angles

Definition at line 332 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_prob_withinrot ( core::Real prob_withinrot)

set the probability of sampling within the same rotamer

Definition at line 346 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_record_statistics ( bool record_statistics)

set whether to record mover statistics or not

Definition at line 411 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_require_mm_bend ( bool require_mm_bend)

set whether to exit during initialize_simulation if the mm_bend term isn't turned on

Definition at line 389 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_statistics_filename ( std::string const & statistics_filename)

set filename for statistics output

Definition at line 427 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::set_task_factory ( core::pack::task::TaskFactoryOP task_factory)

Definition at line 317 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::setup_histograms ( )

private

Definition at line 451 of file BackrubSidechainMover.cc.

std::string const & protocols::backrub::BackrubSidechainMover::statistics_filename ( ) const

get filename for statistics output

Definition at line 421 of file BackrubSidechainMover.cc.

core::pack::task::TaskFactoryCOP protocols::backrub::BackrubSidechainMover::task_factory ( ) const

Definition at line 311 of file BackrubSidechainMover.cc.

utility::vector1< core::id::TorsionID_Range > protocols::backrub::BackrubSidechainMover::torsion_id_ranges ( core::pose::Pose & pose)

virtual

get the TorsionIDs perturbed by the mover during moves, along with their ranges

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 397 of file BackrubSidechainMover.cc.

void protocols::backrub::BackrubSidechainMover::update_segments ( core::pose::Pose const & pose)

Definition at line 191 of file BackrubSidechainMover.cc.

References core::pose::Pose::fold_tree(), and core::pose::Pose::residue().

void protocols::backrub::BackrubSidechainMover::update_type ( )

private

Definition at line 522 of file BackrubSidechainMover.cc.

References protocols::motifs::mt().

Member Data Documentation

utility::vector1<numeric::MultiDimensionalHistogram> protocols::backrub::BackrubSidechainMover::accept_hists_

private

Definition at line 237 of file BackrubSidechainMover.hh.

protocols::backrub::BackrubMoverOP protocols::backrub::BackrubSidechainMover::backrub_mover_

private

Definition at line 228 of file BackrubSidechainMover.hh.

Referenced by BackrubSidechainMover().

core::Real protocols::backrub::BackrubSidechainMover::last_chi1_post_

private

Definition at line 233 of file BackrubSidechainMover.hh.

core::Real protocols::backrub::BackrubSidechainMover::last_chi1_pre_

private

Definition at line 232 of file BackrubSidechainMover.hh.

core::Size protocols::backrub::BackrubSidechainMover::last_valid_segment_index_

private

Definition at line 231 of file BackrubSidechainMover.hh.

utility::vector1<numeric::MultiDimensionalHistogram> protocols::backrub::BackrubSidechainMover::proposal_hists_

private

Definition at line 236 of file BackrubSidechainMover.hh.

bool protocols::backrub::BackrubSidechainMover::record_statistics_

private

Definition at line 234 of file BackrubSidechainMover.hh.

protocols::simple_moves::sidechain_moves::SidechainMoverOP protocols::backrub::BackrubSidechainMover::sidechain_mover_

private

Definition at line 229 of file BackrubSidechainMover.hh.

Referenced by BackrubSidechainMover().

std::string protocols::backrub::BackrubSidechainMover::statistics_filename_

private

Definition at line 235 of file BackrubSidechainMover.hh.

utility::vector1<core::Size> protocols::backrub::BackrubSidechainMover::valid_segments_

private

Definition at line 230 of file BackrubSidechainMover.hh.

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

src/protocols/backrub/BackrubSidechainMover.hh
src/protocols/backrub/BackrubSidechainMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation