#include <WidthFirstSlidingWindowLoopClosure.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure:

Public Member Functions
	WidthFirstSlidingWindowLoopClosure (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn, core::kinematics::MoveMapCOP movemap)
	constructor: supply fragsets for fragment moves More...

	WidthFirstSlidingWindowLoopClosure ()

void	sample_loops (core::pose::Pose &more_cut, core::pose::Pose &less_cut) override

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_closure::ccd::SlidingWindowLoopClosure
	SlidingWindowLoopClosure (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn, core::kinematics::MoveMapCOP movemap)
	constructor: supply fragsets for fragment moves More...

	SlidingWindowLoopClosure ()

	~SlidingWindowLoopClosure () override

virtual void	apply (core::pose::Pose &more_cut, core::pose::Pose &less_cut)

virtual void	select_final_loop (core::pose::Pose &more_cut, core::pose::Pose &less_cut)

void	apply (core::pose::Pose &more_cut) override
	Main Method. More...

core::fragment::FragSetCOP	closure_fragments () const

void	keep_fragments (bool setting=true)

void	output_debug_structure (core::pose::Pose &pose, std::string prefix)

core::kinematics::MoveMap const &	movemap () const

void	movemap (core::kinematics::MoveMapCOP movemap)

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

void	scorefxn (core::scoring::ScoreFunctionOP sfxn)

void	fragments (core::fragment::FragSetCOP frags)

void	scored_frag_cycle_ratio (core::Real setting)

void	short_frag_cycle_ratio (core::Real setting)

void	set_bIdealLoopClosing (bool setting)

bool	bIdealLoopClosing () const

void	set_chainbreak_max (core::Real setting)

void	set_evaluation (evaluation::MetaPoseEvaluatorOP ev)

void	set_loop (Loop const &loop_in)

Loop	determine_loop (core::pose::Pose const &more_cut, core::pose::Pose &less_cut)

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 MoverOP	clone () const
	Return a clone of the Mover object. 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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
static void	setPoseExtraScore (core::pose::Pose &pose)

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
void	set_defaults ()

Protected Member Functions inherited from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
void	generate_window_list (core::Size loop_size, WindowList &window_list) const

void	set_defaults ()

core::scoring::ScoreFunctionOP	setup_frag_scorefxn ()

core::Size	process_fragments (core::fragment::FrameList &frame_in, core::pose::Pose const &more_cut, core::pose::Pose const &loop_pose)
	process fragments for loop-closing prowess, keep track of best_fragment return nr_of new good_loops ( vdw criterion ) More...

bool	bQuickTest () const

core::Real	filter_score (core::pose::Pose &pose)
	return the score used for filtering ( scorefxn_ + filter_cst_weight_ * filter_cst_ ) 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
core::Real	window_acceptance_ratio_

core::Size	nr_scored_sampling_passes_

core::Size	min_fast_loops_

core::Size	min_breakout_fast_loops_

core::Size	nr_scored_fragments_

core::Size	give_up_

Protected Attributes inherited from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
Loop	loop_

core::scoring::ScoreFunctionOP	scorefxn_

core::kinematics::MoveMapCOP	movemap_

core::fragment::FragSetCOP	fragset_

core::fragment::SecondaryStructureOP	ss_info_

core::Size	min_loop_size_

core::Size	max_loop_size_

core::Size	min_good_loops_

core::Size	min_breakout_good_loops_

core::Real	vdw_delta_

core::Real	chainbreak_max_

core::Real	score_delta_

core::Real	scored_frag_cycle_ratio_

core::Real	short_frag_cycle_ratio_

core::scoring::ScoreType	vdw_score_type_

bool	bKeepFragments_

core::fragment::OrderedFragSetOP	closure_fragments_

core::Real	best_score_

core::fragment::FragID	best_fragment_

bool	bQuickTest_

bool	bIdealLoopClosing_

evaluation::MetaPoseEvaluatorOP	evaluator_

constraints_additional::ConstraintEvaluatorOP	filter_cst_

core::Real	filter_cst_weight_

Private Types
typedef SlidingWindowLoopClosure	Parent

Additional Inherited Members
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

Protected Types inherited from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
typedef std::list< std::pair < core::Real, Loop > >	WindowList

Detailed Description

it will switch between different windows. If nothing good is found after one sweep of window sizes we bail out... (assuming that it is fruitless) if things look promising more sampling time is spend to find a good loop

Member Typedef Documentation

typedef SlidingWindowLoopClosure protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::Parent

private

Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::WidthFirstSlidingWindowLoopClosure	(	core::fragment::FragSetCOP	fragset,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::kinematics::MoveMapCOP	movemap
	)

constructor: supply fragsets for fragment moves

References set_defaults().

protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::WidthFirstSlidingWindowLoopClosure ( )

References set_defaults().

Member Function Documentation

std::string protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure.

Reimplemented in protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure.

void protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::register_options ( )

static

void protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops	(	core::pose::Pose &	more_cut,
		core::pose::Pose &	less_cut
	)

overridevirtual

Reimplemented from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure.

void protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::set_defaults ( )

protected

References protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::chainbreak_max_, give_up_, min_breakout_fast_loops_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_breakout_good_loops_, min_fast_loops_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_good_loops_, nr_scored_fragments_, nr_scored_sampling_passes_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_defaults(), protocols::loops::loop_closure::ccd::tr(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::vdw_delta_, and window_acceptance_ratio_.

Referenced by protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::set_defaults(), and WidthFirstSlidingWindowLoopClosure().

Member Data Documentation

core::Size protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::give_up_

protected

Referenced by sample_loops(), and set_defaults().

core::Size protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::min_breakout_fast_loops_

protected

Referenced by sample_loops(), and set_defaults().

core::Size protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::min_fast_loops_

protected

Referenced by sample_loops(), and set_defaults().

core::Size protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::nr_scored_fragments_

protected

Referenced by sample_loops(), and set_defaults().

core::Size protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::nr_scored_sampling_passes_

protected

Referenced by sample_loops(), and set_defaults().

core::Real protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::window_acceptance_ratio_

protected

Referenced by sample_loops(), and set_defaults().

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

src/protocols/loops/loop_closure/ccd/WidthFirstSlidingWindowLoopClosure.hh
src/protocols/loops/loop_closure/ccd/WidthFirstSlidingWindowLoopClosure.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation