#include <SlidingWindowLoopClosure.hh>

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

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

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

virtual void	sample_loops (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)

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	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...

Protected Types
typedef std::list< std::pair < core::Real, Loop > >	WindowList

Protected Member Functions
void	generate_window_list (Size loop_size, WindowList &window_list) const

void	set_defaults ()

void	setup_frag_scorefxn (core::scoring::ScoreFunction &scorefxn)

Size	process_fragments (core::fragment::FrameList &frame_in, core::pose::Pose const &more_cut, core::pose::Pose const &loop_pose)

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
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_

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

Detailed Description

Definition at line 72 of file SlidingWindowLoopClosure.hh.

Member Typedef Documentation

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

protected

Definition at line 175 of file SlidingWindowLoopClosure.hh.

Constructor & Destructor Documentation

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

Definition at line 104 of file SlidingWindowLoopClosure.cc.

References set_defaults().

protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::SlidingWindowLoopClosure ( )

Definition at line 116 of file SlidingWindowLoopClosure.cc.

References set_defaults().

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

Definition at line 125 of file SlidingWindowLoopClosure.cc.

Member Function Documentation

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply	(	core::pose::Pose &	more_cut,
		core::pose::Pose &	less_cut
	)

virtual

Definition at line 291 of file SlidingWindowLoopClosure.cc.

References protocols::loops::add_single_cutpoint_variant(), closure_fragments(), protocols::evaluation::evaluate_pose(), evaluator_, core::pose::Pose::fold_tree(), loop_, protocols::loops::remove_cutpoint_variants(), sample_loops(), scorefxn_, select_final_loop(), setPoseExtraScores(), setup_frag_scorefxn(), and protocols::loops::loop_closure::ccd::tr().

Referenced by apply().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply ( core::pose::Pose & more_cut)

virtual

Implements protocols::moves::Mover.

Definition at line 269 of file SlidingWindowLoopClosure.cc.

References apply(), and bIdealLoopClosing().

bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bIdealLoopClosing ( ) const

inline

Definition at line 156 of file SlidingWindowLoopClosure.hh.

References bIdealLoopClosing_.

Referenced by apply(), and process_fragments().

bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bQuickTest ( ) const

inlineprotected

Definition at line 216 of file SlidingWindowLoopClosure.hh.

References bQuickTest_.

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

core::fragment::FragSetCOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::closure_fragments ( ) const

inline

Definition at line 108 of file SlidingWindowLoopClosure.hh.

References closure_fragments_.

Referenced by apply(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), and select_final_loop().

Loop protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop	(	core::pose::Pose const &	more_cut,
		core::pose::Pose &	less_cut
	)

Definition at line 174 of file SlidingWindowLoopClosure.cc.

References core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get_bb(), movemap(), and protocols::loops::loop_closure::ccd::tr().

Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::filter_score ( core::pose::Pose & pose)

protected

return the score used for filtering ( scorefxn_ + filter_cst_weight_ * filter_cst_ )

Definition at line 497 of file SlidingWindowLoopClosure.cc.

References filter_cst_, filter_cst_weight_, and scorefxn_.

Referenced by process_fragments().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragments ( core::fragment::FragSetCOP frags)

inline

Definition at line 137 of file SlidingWindowLoopClosure.hh.

References fragset_, and ss_info_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list	(	Size	loop_size,
		WindowList &	window_list
	)		const

protected

Definition at line 604 of file SlidingWindowLoopClosure.cc.

References protocols::loops::Loop::cut(), loop_, ss_info_, protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::loops::loop_closure::ccd::tr().

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

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure, and protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure.

Definition at line 277 of file SlidingWindowLoopClosure.cc.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::keep_fragments ( bool setting = true)

inline

Definition at line 112 of file SlidingWindowLoopClosure.hh.

References bKeepFragments_.

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

core::kinematics::MoveMap const& protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap ( ) const

inline

Definition at line 120 of file SlidingWindowLoopClosure.hh.

References movemap_.

Referenced by determine_loop(), movemap(), process_fragments(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), and select_final_loop().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap ( core::kinematics::MoveMapCOP movemap)

Definition at line 128 of file SlidingWindowLoopClosure.cc.

References movemap(), and movemap_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::output_debug_structure	(	core::pose::Pose &	pose,
		std::string	prefix
	)

Definition at line 151 of file SlidingWindowLoopClosure.cc.

References protocols::moves::Mover::get_current_job(), protocols::moves::Mover::get_current_tag(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop().

Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments	(	core::fragment::FrameList &	frame_in,
		core::pose::Pose const &	more_cut,
		core::pose::Pose const &	loop_pose
	)

protected

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

virtual

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

Definition at line 330 of file SlidingWindowLoopClosure.cc.

Referenced by apply().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scored_frag_cycle_ratio ( core::Real setting)

inline

Definition at line 143 of file SlidingWindowLoopClosure.hh.

References scored_frag_cycle_ratio_.

Referenced by protocols::loop_build::LoopMover_SlidingWindow::model_loop().

core::scoring::ScoreFunction const& protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn ( ) const

inline

Definition at line 127 of file SlidingWindowLoopClosure.hh.

References scorefxn_.

Referenced by protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn ( core::scoring::ScoreFunctionOP sfxn)

inline

Definition at line 131 of file SlidingWindowLoopClosure.hh.

References scorefxn_.

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

virtual

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

Definition at line 449 of file SlidingWindowLoopClosure.cc.

References core::fragment::FragID::apply(), best_fragment_, closure_fragments(), core::sequence::end, protocols::moves::Mover::get_current_tag(), core::fragment::FragID::is_valid(), loop_, movemap(), protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE, core::pose::setPoseExtraScores(), protocols::loops::Loop::size(), protocols::loops::loop_closure::ccd::tr(), and protocols::loops::loop_closure::ccd::VDW_FRAG_STORE.

Referenced by apply().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_bIdealLoopClosing ( bool setting)

inline

Definition at line 152 of file SlidingWindowLoopClosure.hh.

References bIdealLoopClosing_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_chainbreak_max ( core::Real setting)

inline

Definition at line 160 of file SlidingWindowLoopClosure.hh.

References chainbreak_max_.

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

protected

Definition at line 133 of file SlidingWindowLoopClosure.cc.

References bIdealLoopClosing_, bKeepFragments_, bQuickTest_, chainbreak_max_, max_loop_size_, min_breakout_good_loops_, min_good_loops_, min_loop_size_, score_delta_, scored_frag_cycle_ratio_, short_frag_cycle_ratio_, protocols::loops::loop_closure::ccd::tr(), core::scoring::vdw, vdw_delta_, and vdw_score_type_.

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

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_evaluation ( evaluation::MetaPoseEvaluatorOP ev)

inline

Definition at line 165 of file SlidingWindowLoopClosure.hh.

References evaluator_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_loop ( Loop const & loop_in)

inline

Definition at line 168 of file SlidingWindowLoopClosure.hh.

References loop_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setPoseExtraScores ( core::pose::Pose & pose)

static

Definition at line 282 of file SlidingWindowLoopClosure.cc.

References core::pose::setPoseExtraScores().

Referenced by protocols::abinitio::AbrelaxMover::apply(), and apply().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setup_frag_scorefxn ( core::scoring::ScoreFunction & scorefxn)

protected

Definition at line 224 of file SlidingWindowLoopClosure.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), filter_cst_, filter_cst_weight_, core::scoring::linear_chainbreak, core::scoring::overlap_chainbreak, scorefxn_, and protocols::loops::loop_closure::ccd::tr().

Referenced by apply(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and sample_loops().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio ( core::Real setting)

inline

Definition at line 147 of file SlidingWindowLoopClosure.hh.

References short_frag_cycle_ratio_.

Member Data Documentation

core::fragment::FragID protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::best_fragment_

protected

Definition at line 255 of file SlidingWindowLoopClosure.hh.

Referenced by process_fragments(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), sample_loops(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), and select_final_loop().

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::best_score_

protected

Definition at line 254 of file SlidingWindowLoopClosure.hh.

Referenced by process_fragments(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), sample_loops(), and protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop().

bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bIdealLoopClosing_

protected

Definition at line 262 of file SlidingWindowLoopClosure.hh.

Referenced by bIdealLoopClosing(), set_bIdealLoopClosing(), and set_defaults().

bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bKeepFragments_

protected

Definition at line 251 of file SlidingWindowLoopClosure.hh.

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

bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bQuickTest_

protected

Definition at line 257 of file SlidingWindowLoopClosure.hh.

Referenced by bQuickTest(), and set_defaults().

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::chainbreak_max_

protected

Definition at line 245 of file SlidingWindowLoopClosure.hh.

Referenced by process_fragments(), sample_loops(), set_chainbreak_max(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::set_defaults(), and set_defaults().

core::fragment::OrderedFragSetOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::closure_fragments_

protected

Definition at line 252 of file SlidingWindowLoopClosure.hh.

Referenced by closure_fragments(), process_fragments(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and sample_loops().

evaluation::MetaPoseEvaluatorOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::evaluator_

protected

Definition at line 264 of file SlidingWindowLoopClosure.hh.

Referenced by apply(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), sample_loops(), and set_evaluation().

constraints_additional::ConstraintEvaluatorOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::filter_cst_

protected

Definition at line 266 of file SlidingWindowLoopClosure.hh.

Referenced by filter_score(), and setup_frag_scorefxn().

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::filter_cst_weight_

protected

Definition at line 267 of file SlidingWindowLoopClosure.hh.

Referenced by filter_score(), and setup_frag_scorefxn().

core::fragment::FragSetCOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragset_

protected

Definition at line 236 of file SlidingWindowLoopClosure.hh.

Referenced by fragments(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and sample_loops().

Loop protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::loop_

protected

Definition at line 226 of file SlidingWindowLoopClosure.hh.

Referenced by apply(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), generate_window_list(), process_fragments(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), sample_loops(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), select_final_loop(), and set_loop().

core::Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::max_loop_size_

protected

Definition at line 241 of file SlidingWindowLoopClosure.hh.

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

core::Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_breakout_good_loops_

protected

Definition at line 243 of file SlidingWindowLoopClosure.hh.

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

core::Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_good_loops_

protected

Definition at line 242 of file SlidingWindowLoopClosure.hh.

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

core::Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_loop_size_

protected

Definition at line 240 of file SlidingWindowLoopClosure.hh.

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

core::kinematics::MoveMapCOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap_

protected

Definition at line 231 of file SlidingWindowLoopClosure.hh.

Referenced by movemap(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and sample_loops().

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::score_delta_

protected

Definition at line 246 of file SlidingWindowLoopClosure.hh.

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

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scored_frag_cycle_ratio_

protected

Definition at line 247 of file SlidingWindowLoopClosure.hh.

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

core::scoring::ScoreFunctionOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn_

protected

Definition at line 228 of file SlidingWindowLoopClosure.hh.

Referenced by apply(), filter_score(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), scorefxn(), and setup_frag_scorefxn().

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio_

protected

Definition at line 248 of file SlidingWindowLoopClosure.hh.

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

core::fragment::SecondaryStructureOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::ss_info_

protected

Definition at line 238 of file SlidingWindowLoopClosure.hh.

Referenced by fragments(), and generate_window_list().

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::vdw_delta_

protected

Definition at line 244 of file SlidingWindowLoopClosure.hh.

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

core::scoring::ScoreType protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::vdw_score_type_

protected

Definition at line 249 of file SlidingWindowLoopClosure.hh.

Referenced by process_fragments(), and set_defaults().

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

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

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