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

#include <LoopMover_SlidingWindow.hh>

Inheritance diagram for protocols::loop_build::LoopMover_SlidingWindow:

Collaboration diagram for protocols::loop_build::LoopMover_SlidingWindow:

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

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

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

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

virtual protocols::moves::MoverOP	clone () const
	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...

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

	IndependentLoopMover (LoopsOP loops_in)

	IndependentLoopMover (LoopsFileData const &lfd)

	IndependentLoopMover (GuardedLoopsFromFileOP guarded_loops)

virtual	~IndependentLoopMover ()

void	set_defaults ()

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

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...

virtual	~LoopMover ()

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::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

std::string	torsion_features_string (core::pose::Pose const &pose) const
	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 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

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

virtual basic::Tracer &	tr () const

Protected Attributes
std::vector < core::fragment::ConstantLengthFragSetOP >	frag_libs_
	list of fragment libraries to use More...

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

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

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

Definition at line 42 of file LoopMover_SlidingWindow.hh.

Constructor & Destructor Documentation

protocols::loop_build::LoopMover_SlidingWindow::LoopMover_SlidingWindow ( )

Loops constructor.

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

Definition at line 67 of file LoopMover_SlidingWindow.cc.

References core::scoring::chainbreak, 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().

Referenced by clone().

protocols::loop_build::LoopMover_SlidingWindow::LoopMover_SlidingWindow ( protocols::loops::LoopsOP loops_in)

Loops constructor.

Parameters

[in]	loops_in	the set of loops to model
[in]	frags_from_file	read fragments from files specified on command line?

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

Definition at line 78 of file LoopMover_SlidingWindow.cc.

References core::scoring::chainbreak, 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().

protocols::loop_build::LoopMover_SlidingWindow::LoopMover_SlidingWindow	(	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
[in]	frags_from_file	read fragments from files specified on command line?

Definition at line 91 of file LoopMover_SlidingWindow.cc.

References core::scoring::chainbreak, 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().

Member Function Documentation

virtual protocols::moves::MoverOP protocols::loop_build::LoopMover_SlidingWindow::clone ( ) const

inlinevirtual

clone this object

Reimplemented from protocols::moves::Mover.

Definition at line 77 of file LoopMover_SlidingWindow.hh.

References LoopMover_SlidingWindow().

std::string protocols::loop_build::LoopMover_SlidingWindow::get_name ( ) const

virtual

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

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

Definition at line 200 of file LoopMover_SlidingWindow.cc.

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