#include <FASelectSlidingWindowLoopClosure.hh>

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

Collaboration diagram for protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure:

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

	FASelectSlidingWindowLoopClosure ()

	~FASelectSlidingWindowLoopClosure ()

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

void	set_defaults ()

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

core::Real	fascore (core::pose::Pose &fa_pose) const

void	set_fullatom_pose (core::pose::Pose &fa_pose)

Public Member Functions inherited from 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 More...

	WidthFirstSlidingWindowLoopClosure ()

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

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 ()

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

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

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	~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 MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

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

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
static void	register_options ()

Static Public Member Functions inherited from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
static void	setPoseExtraScores (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. 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...

Private Types
typedef WidthFirstSlidingWindowLoopClosure	Parent

Private Attributes
core::pose::PoseOP	fa_pose_

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

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

Protected Member Functions inherited from protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
void	set_defaults ()

Protected Attributes inherited from protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
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_

Detailed Description

Definition at line 68 of file FASelectSlidingWindowLoopClosure.hh.

Member Typedef Documentation

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

private

Definition at line 69 of file FASelectSlidingWindowLoopClosure.hh.

Constructor & Destructor Documentation

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

constructor: supply fragsets for fragment moves

Definition at line 94 of file FASelectSlidingWindowLoopClosure.cc.

References set_defaults().

protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::FASelectSlidingWindowLoopClosure ( )

Definition at line 103 of file FASelectSlidingWindowLoopClosure.cc.

References set_defaults().

protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::~FASelectSlidingWindowLoopClosure ( )

Definition at line 109 of file FASelectSlidingWindowLoopClosure.cc.

Member Function Documentation

core::Real protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore ( core::pose::Pose & fa_pose) const

Definition at line 252 of file FASelectSlidingWindowLoopClosure.cc.

References protocols::loops::Loops::add_loop(), protocols::relax::FastRelax::apply(), core::scoring::getScoreFunction(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::loop_, protocols::loops::loops_set_move_map(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn(), and protocols::relax::RelaxProtocolBase::set_movemap().

Referenced by select_final_loop().

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

virtual

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

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

Definition at line 112 of file FASelectSlidingWindowLoopClosure.cc.

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

static

Definition at line 122 of file FASelectSlidingWindowLoopClosure.cc.

void protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop	(	core::pose::Pose &	more_cut,
		core::pose::Pose &	less_cut
	)