The loop-rebuild protocol. More...

#include <LoopMover.hh>

Public Types
typedef core::kinematics::MoveMapOP	MoveMapOP

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
	LoopMover ()

	LoopMover (protocols::loops::LoopsOP loops_in)

	LoopMover (protocols::loops::LoopsFileData const &loops_from_file)

	LoopMover (protocols::loops::GuardedLoopsFromFileOP guarded_loops)

	LoopMover (LoopMover const &rhs)
	copy ctor More...

LoopMover &	operator= (LoopMover const &rhs)
	assignment operator More...

virtual	~LoopMover ()

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

void	set_guarded_loops_not_in_charge ()
	Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply() More...

virtual void	apply (core::pose::Pose &)=0
	Apply the loop-build protocol to the input pose. More...

void	set_scorefxn (const core::scoring::ScoreFunctionOP score_in)

const core::scoring::ScoreFunctionOP &	scorefxn () const

void	loops (protocols::loops::LoopsOP lptr)
	Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data. More...

void	loops (LoopsFileData const &loop_file_data)
	Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ). More...

void	loops (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
	Set the guarded_loops pointer. More...

protocols::loops::LoopsCOP	loops () const
	Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...

protocols::loops::LoopsOP	loops ()
	non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...

const utility::vector1 < core::fragment::FragSetOP > &	frag_libs () const

core::conformation::torsion_bin_string	torsion_features_string (core::pose::Pose const &pose) const
	create a string representing the torsion bins (ABEGX) for the loops defined in the guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there's only one Loop object in the guarded_loops_ object). More...

virtual void	set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
	Extend a loop. More...

void	add_fragments (core::fragment::FragSetOP fragset)
	add a fragment set More...

void	clear_fragments ()
	clear the list of fragment sets More...

MoveMapOP const &	false_movemap () const
	explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...

void	false_movemap (MoveMapOP const &mm)
	explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...

checkpoint::CheckPointerOP &	get_checkpoints ()

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

void	set_type (std::string const &setting)

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
	Return a clone of the Mover object. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Protected Member Functions
Size	enforce_false_movemap (MoveMapOP &mm) const
	import the false_movemap's explicit False settings into the given MoveMap More...

void	set_loops_from_pose_observer_cache (core::pose::Pose const &pose)
	allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step More...

bool	use_loops_from_observer_cache () const

void	set_use_loops_from_observer_cache (bool const loops_from_observer_cache)

virtual basic::Tracer &	tr () const =0

void	resolve_loop_indices (core::pose::Pose const &p)
	Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply. 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 Member Functions
void	init ()

void	initForEqualOperatorAndCopyConstructor (LoopMover &lhs, LoopMover const &rhs)

Private Attributes
GuardedLoopsFromFileOP	guarded_loops_

core::scoring::ScoreFunctionOP	scorefxn_

utility::vector1 < core::fragment::FragSetOP >	frag_libs_

checkpoint::CheckPointerOP	checkpoints_

bool	loops_from_observer_cache_

MoveMapOP	false_movemap_
	explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...

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...

Detailed Description

The loop-rebuild protocol.

Member Typedef Documentation

typedef core::kinematics::MoveMapOP protocols::loops::loop_mover::LoopMover::MoveMapOP

Constructor & Destructor Documentation

protocols::loops::loop_mover::LoopMover::LoopMover ( )

References init().

protocols::loops::loop_mover::LoopMover::LoopMover ( protocols::loops::LoopsOP loops_in )

GuardedLoops constructed with a pointer to a loops object: sets the GuardedLoops object into it's "not in charge" mode; i.e. the external source of the LoopsOP is responsible for resolving loop indices

References init().

protocols::loops::loop_mover::LoopMover::LoopMover ( protocols::loops::LoopsFileData const & loops_from_file )

GuardedLoops constructed with an unresolve-loop-indices object: sets the GuardedLoops object into it's "in charge" mode; i.e. before the loops object may be used, the loop indices must be resolved.

References init().

protocols::loops::loop_mover::LoopMover::LoopMover ( protocols::loops::GuardedLoopsFromFileOP guarded_loops )

References init().

protocols::loops::loop_mover::LoopMover::LoopMover ( LoopMover const & rhs )

copy ctor

References initForEqualOperatorAndCopyConstructor().

protocols::loops::loop_mover::LoopMover::~LoopMover ( )

virtual

Member Function Documentation

void protocols::loops::loop_mover::LoopMover::add_fragments ( core::fragment::FragSetOP fragset )

add a fragment set

References core::fragment::FragSet::clone(), and frag_libs_.

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::LoopMover_Perturb_CCD(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD().

virtual void protocols::loops::loop_mover::LoopMover::apply ( core::pose::Pose & )

pure virtual

Apply the loop-build protocol to the input pose.

Implements protocols::moves::Mover.

Implemented in protocols::loops::loop_mover::refine::LoopMover_Refine_CCD, protocols::loops::loop_mover::refine::LoopMover_Refine_KIC, protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub, and protocols::loops::loop_mover::IndependentLoopMover.

void protocols::loops::loop_mover::LoopMover::clear_fragments ( )

clear the list of fragment sets

References frag_libs_.

Size protocols::loops::loop_mover::LoopMover::enforce_false_movemap ( MoveMapOP & mm ) const

protected

import the false_movemap's explicit False settings into the given MoveMap

Returns: The number of False settings imported.

References false_movemap(), and core::kinematics::MoveMap::import_false().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap().

LoopMover::MoveMapOP const & protocols::loops::loop_mover::LoopMover::false_movemap ( ) const

explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol

References false_movemap_.

Referenced by protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), and enforce_false_movemap().

void protocols::loops::loop_mover::LoopMover::false_movemap ( MoveMapOP const & mm )

explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol

References false_movemap_.

const utility::vector1< core::fragment::FragSetOP > & protocols::loops::loop_mover::LoopMover::frag_libs ( ) const

References frag_libs_.

Referenced by protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop().

checkpoint::CheckPointerOP & protocols::loops::loop_mover::LoopMover::get_checkpoints ( )

References checkpoints_.

Referenced by protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), and protocols::loop_build::LoopMover_SlidingWindow::model_loop().

std::string protocols::loops::loop_mover::LoopMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::loops::loop_mover::LoopMover::init ( void )

private

References checkpoints_, false_movemap_, and loops_from_observer_cache_.

Referenced by LoopMover(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC().

void protocols::loops::loop_mover::LoopMover::initForEqualOperatorAndCopyConstructor	(	LoopMover &	lhs,
		LoopMover const &	rhs
	)

private

References checkpoints_, false_movemap_, frag_libs_, guarded_loops_, loops_from_observer_cache_, and scorefxn_.

Referenced by LoopMover(), and operator=().

void protocols::loops::loop_mover::LoopMover::loops ( protocols::loops::LoopsOP lptr )

Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data.

References guarded_loops_.

void protocols::loops::loop_mover::LoopMover::loops ( LoopsFileData const & loop_file_data )

Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).

References guarded_loops_.

void protocols::loops::loop_mover::LoopMover::loops ( protocols::loops::GuardedLoopsFromFileOP guarded_loops )

Set the guarded_loops pointer.

References guarded_loops_.

protocols::loops::LoopsCOP protocols::loops::loop_mover::LoopMover::loops ( ) const

Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called.

References guarded_loops_.

protocols::loops::LoopsOP protocols::loops::loop_mover::LoopMover::loops ( )

non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called.

References guarded_loops_.

LoopMover & protocols::loops::loop_mover::LoopMover::operator= ( LoopMover const & rhs )

assignment operator

References initForEqualOperatorAndCopyConstructor().

void protocols::loops::loop_mover::LoopMover::resolve_loop_indices ( core::pose::Pose const & p )

protected

Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply.

References guarded_loops_.

Referenced by protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), and protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply().

const core::scoring::ScoreFunctionOP & protocols::loops::loop_mover::LoopMover::scorefxn ( ) const

References scorefxn_.

void protocols::loops::loop_mover::LoopMover::set_extended_torsions	(	core::pose::Pose &	pose,
		Loop const &	loop
	)

virtual

Extend a loop.

Set a loop to extended torsion angles.

Reimplemented in protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC.

References protocols::loops::idealize_loop(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and tr().

Referenced by protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop().

void protocols::loops::loop_mover::LoopMover::set_guarded_loops_not_in_charge ( )

Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply()

References guarded_loops_.

void protocols::loops::loop_mover::LoopMover::set_loops_from_pose_observer_cache ( core::pose::Pose const & pose )

protected

allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step

Author: flo, march 2011

References protocols::loops::Loops::add_loop(), guarded_loops_, loops(), core::pose::Pose::observer_cache(), numeric::random::random_range(), core::pose::datacache::CacheableObserverType::SPECIAL_SEGMENTS_OBSERVER, utility::pointer::static_pointer_cast(), tr(), and utility_exit_with_message.

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply().

void protocols::loops::loop_mover::LoopMover::set_scorefxn ( const core::scoring::ScoreFunctionOP score_in )

References scorefxn_.

Referenced by protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::init(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::LoopMover_Perturb_CCD(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::LoopMover_Perturb_KIC(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::LoopMover_Refine_Backrub(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD(), protocols::loop_build::LoopMover_SlidingWindow::LoopMover_SlidingWindow(), and protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag().

void protocols::loops::loop_mover::LoopMover::set_use_loops_from_observer_cache ( bool const loops_from_observer_cache )

protected

References loops_from_observer_cache_.

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag().

core::conformation::torsion_bin_string protocols::loops::loop_mover::LoopMover::torsion_features_string ( core::pose::Pose const & pose ) const

create a string representing the torsion bins (ABEGX) for the loops defined in the guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there's only one Loop object in the guarded_loops_ object).

bin torsion angles as described in http://www.ncbi.nlm.nih.gov/pubmed/19646450

generates a string with the torsion angle bins, using uppercase letters as in the publication above for omega ~ 180, and lowercase letters for omega ~ 0; to be used in loop sampling analysis