LoopMover utilizing fragment insertion, ccd loop closure, and minimization. More...

#include <LoopMover_QuickCCD.hh>

Inheritance diagram for protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD:

[legend]

Public Member Functions
	LoopMover_Perturb_QuickCCD ()
	Loops constructor. More...

	LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in)
	Loops constructor. More...

	LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn)
	Loops & ScoreFunction constructor. More...

	LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn, core::fragment::FragSetOP fragset)
	Loops & ScoreFunction constructor. More...

	~LoopMover_Perturb_QuickCCD () override

protocols::moves::MoverOP	clone () const override
	clone this object More...

bool	randomize_loop () const
	randomize loops prior to loop modeling? More...

void	randomize_loop (bool const flag)
	indicate whether loops should be randomized prior to modeling More...

void	set_default_settings ()
	set default settings More...

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

Public Member Functions inherited from protocols::loops::loop_mover::IndependentLoopMover
	IndependentLoopMover ()

	IndependentLoopMover (LoopsOP loops_in)

	IndependentLoopMover (utility::vector1< bool > const &selection)

	IndependentLoopMover (LoopsFileData const &lfd)

	IndependentLoopMover (GuardedLoopsFromFileOP guarded_loops)

	~IndependentLoopMover () override

void	set_defaults ()

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

void	set_build_attempts_ (int value)
	Accessors: More...

void	set_grow_attempts_ (int value)

void	set_accept_aborted_loops_ (bool value)

void	set_strict_loops (bool value)

void	set_random_order_ (bool value)

void	set_build_all_loops_ (bool value)

void	set_loop_combine_rate_ (core::Real value)

int	get_build_attempts () const

int	get_grow_attempts () const

bool	get_accept_aborted_loops () const

bool	get_strict_loops () const

bool	get_random_order () const

bool	get_build_all_loops () const

bool	get_loop_combine_rate () const

bool	get_all_loops_closed () const

LoopResult	get_last_LoopResult () const

Public Member Functions inherited from protocols::loops::loop_mover::LoopMover
	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...

	~LoopMover () override

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...

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::loops_definers::LoopsDefinerOP setting)

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 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

Static Public Member Functions
static std::string	mover_name ()

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

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
LoopResult	model_loop (core::pose::Pose &pose, protocols::loops::Loop const &loop) override
	loop modeling protocol implementation More...

basic::Tracer &	tr () const override

Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover
core::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)

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...

Protected Attributes
bool	randomize_loop_
	randomize loops prior to performing loop modeling? More...

Additional Inherited Members
Public Types inherited from protocols::loops::loop_mover::LoopMover
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 std::list< std::string >	Strings

Detailed Description

LoopMover utilizing fragment insertion, ccd loop closure, and minimization.

Constructor & Destructor Documentation

◆ LoopMover_Perturb_QuickCCD() [1/4]

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( )

Loops constructor.

Remarks: Will be initialized with centroid level score function 'score4L'.

References protocols::loops::get_cen_scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

◆ LoopMover_Perturb_QuickCCD() [2/4]

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( protocols::loops::LoopsOP loops_in )

Loops constructor.

Parameters

[in] loops_in the set of loops to model

Remarks: Will be initialized with centroid level score function 'score4L'.

References protocols::loops::get_cen_scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

◆ LoopMover_Perturb_QuickCCD() [3/4]

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD	(	protocols::loops::LoopsOP	loops_in,
		core::scoring::ScoreFunctionOP	scorefxn
	)

Loops & ScoreFunction constructor.

Parameters

[in]	loops_in	the set of loops to model
[in]	scorefxn	desired ScoreFunction

References protocols::loops::get_cen_scorefxn(), protocols::loops::loop_mover::LoopMover::scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

◆ LoopMover_Perturb_QuickCCD() [4/4]

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD	(	protocols::loops::LoopsOP	loops_in,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::fragment::FragSetOP	fragset
	)

Loops & ScoreFunction constructor.

Parameters

[in]	loops_in	the set of loops to model
[in]	scorefxn	desired ScoreFunction
[in]	fragset	is the FragSet to be used line?

References protocols::loops::loop_mover::LoopMover::add_fragments(), protocols::loops::get_cen_scorefxn(), protocols::loops::loop_mover::LoopMover::scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

◆ ~LoopMover_Perturb_QuickCCD()

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::~LoopMover_Perturb_QuickCCD ( )

overridedefault

Member Function Documentation

◆ clone()

protocols::moves::MoverOP protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::clone ( ) const

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

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

◆ get_name()

std::string protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::loops::loop_mover::IndependentLoopMover.

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

References mover_name().

◆ model_loop()

LoopResult protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop	(	core::pose::Pose &	pose,
		protocols::loops::Loop const &	loop
	)