#include <SlidingWindowLoopClosure.hh>

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

[legend]

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 () override

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

std::string	get_name () const override
	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)

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

Protected Member Functions
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
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::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Member Typedef Documentation

◆ WindowList

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

protected

Constructor & Destructor Documentation

◆ SlidingWindowLoopClosure() [1/2]

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

References set_defaults().

◆ SlidingWindowLoopClosure() [2/2]

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

References set_defaults().

◆ ~SlidingWindowLoopClosure()

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

overridedefault

Member Function Documentation

◆ apply() [1/2]

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References apply(), and bIdealLoopClosing().

◆ apply() [2/2]

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

virtual

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(), setPoseExtraScore(), setup_frag_scorefxn(), and protocols::loops::loop_closure::ccd::tr().

Referenced by apply().

◆ bIdealLoopClosing()

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

inline

References bIdealLoopClosing_.

Referenced by apply(), and process_fragments().

◆ bQuickTest()

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

inlineprotected

References bQuickTest_.

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

◆ closure_fragments()

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

inline

References closure_fragments_.

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

◆ determine_loop()

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

References core::kinematics::FoldTree::cutpoint(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), movemap(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_cutpoint(), and protocols::loops::loop_closure::ccd::tr().

◆ filter_score()

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_ )

References filter_cst_, filter_cst_weight_, protocols::hybridization::score, and scorefxn_.

Referenced by process_fragments().

◆ fragments()

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

References fragset_, loop_, max_loop_size_, protocols::mean_field::min(), protocols::loops::Loop::size(), ss_info_, and protocols::loops::Loop::start().

◆ generate_window_list()

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

protected

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

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

◆ get_name()

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

overridevirtual

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.

Referenced by set_loop().

◆ keep_fragments()

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

inline

References bKeepFragments_.

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

◆ movemap() [1/2]

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

inline

References movemap_.

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

◆ movemap() [2/2]

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

References movemap(), and movemap_.

Referenced by movemap().

◆ output_debug_structure()

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

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().

◆ process_fragments()

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

process fragments for loop-closing prowess, keep track of best_fragment return nr_of new good_loops ( vdw criterion )

References protocols::loops::Loops::add_loop(), best_fragment_, best_score_, bIdealLoopClosing(), core::scoring::CA_rmsd(), core::scoring::chainbreak, chainbreak_max_, closure_fragments_, core::pose::Pose::energies(), filter_score(), protocols::moves::Mover::get_native_pose(), core::scoring::linear_chainbreak, loop_, protocols::loops::loop_rmsd(), movemap(), core::scoring::overlap_chainbreak, protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE, protocols::hybridization::score, protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE, core::fragment::CacheWrapper< T, XCacheUnit >::store(), core::scoring::Energies::total_energies(), protocols::loops::loop_closure::ccd::tr(), vdw_delta_, protocols::loops::loop_closure::ccd::VDW_FRAG_STORE, and vdw_score_type_.

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

◆ sample_loops()

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.

Referenced by apply().

◆ scored_frag_cycle_ratio()

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

inline

References scored_frag_cycle_ratio_.

◆ scorefxn() [1/2]

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

inline

References scorefxn_.

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

◆ scorefxn() [2/2]

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

inline

References scorefxn_.

◆ select_final_loop()

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.

References core::fragment::FragID::apply(), best_fragment_, closure_fragments(), protocols::moves::Mover::get_current_tag(), core::fragment::FragID::is_valid(), loop_, movemap(), core::fragment::CacheWrapper< T, XCacheUnit >::retrieve(), protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE, core::pose::setPoseExtraScore(), protocols::loops::Loop::size(), protocols::loops::loop_closure::ccd::tr(), and protocols::loops::loop_closure::ccd::VDW_FRAG_STORE.

Referenced by apply().

◆ set_bIdealLoopClosing()

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

inline

References bIdealLoopClosing_.

◆ set_chainbreak_max()

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

inline

References chainbreak_max_.

◆ set_defaults()

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

protected

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().

◆ set_evaluation()

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

inline

References evaluator_.

◆ set_loop()

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

References fragset_, get_name(), loop_, max_loop_size_, protocols::mean_field::min(), protocols::loops::Loop::size(), and protocols::loops::Loop::start().

◆ setPoseExtraScore()

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

static

References core::pose::setPoseExtraScore().

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

◆ setup_frag_scorefxn()

core::scoring::ScoreFunctionOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setup_frag_scorefxn ( )

protected

also modifies the internal scorefxn_ variable (But not necessarily to same function as is returned.)

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

◆ short_frag_cycle_ratio()

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

inline

References short_frag_cycle_ratio_.

Member Data Documentation

◆ best_fragment_

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

protected

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

◆ best_score_

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

protected

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

◆ bIdealLoopClosing_

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

protected

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

◆ bKeepFragments_

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

protected

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

◆ bQuickTest_

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

protected

Referenced by bQuickTest(), and set_defaults().

◆ chainbreak_max_

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

protected

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

◆ closure_fragments_

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

protected

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

◆ evaluator_

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

protected

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

◆ filter_cst_

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

protected

Referenced by filter_score(), and setup_frag_scorefxn().

◆ filter_cst_weight_

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

protected

Referenced by filter_score(), and setup_frag_scorefxn().

◆ fragset_

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

protected

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

◆ loop_

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

protected

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

◆ max_loop_size_

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

protected

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

◆ min_breakout_good_loops_

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

protected

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

◆ min_good_loops_

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

protected

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

◆ min_loop_size_

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

protected

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

◆ movemap_

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

protected

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

◆ score_delta_

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

protected

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

◆ scored_frag_cycle_ratio_

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

protected

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

◆ scorefxn_

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

protected

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

◆ short_frag_cycle_ratio_

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

protected

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

◆ ss_info_

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

protected

Referenced by fragments(), and generate_window_list().

◆ vdw_delta_

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

protected

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

◆ vdw_score_type_

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

protected

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

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Typedef Documentation

◆ WindowList

Constructor & Destructor Documentation

◆ SlidingWindowLoopClosure() [1/2]

◆ SlidingWindowLoopClosure() [2/2]

◆ ~SlidingWindowLoopClosure()

Member Function Documentation

◆ apply() [1/2]

◆ apply() [2/2]

◆ bIdealLoopClosing()

◆ bQuickTest()

◆ closure_fragments()

◆ determine_loop()

◆ filter_score()

◆ fragments()

◆ generate_window_list()

◆ get_name()

◆ keep_fragments()

◆ movemap() [1/2]

◆ movemap() [2/2]

◆ output_debug_structure()

◆ process_fragments()

◆ sample_loops()

◆ scored_frag_cycle_ratio()

◆ scorefxn() [1/2]

◆ scorefxn() [2/2]

◆ select_final_loop()

◆ set_bIdealLoopClosing()

◆ set_chainbreak_max()

◆ set_defaults()

◆ set_evaluation()

◆ set_loop()

◆ setPoseExtraScore()

◆ setup_frag_scorefxn()

◆ short_frag_cycle_ratio()

Member Data Documentation

◆ best_fragment_

◆ best_score_

◆ bIdealLoopClosing_

◆ bKeepFragments_

◆ bQuickTest_

◆ chainbreak_max_

◆ closure_fragments_

◆ evaluator_

◆ filter_cst_

◆ filter_cst_weight_

◆ fragset_

◆ loop_

◆ max_loop_size_

◆ min_breakout_good_loops_

◆ min_good_loops_

◆ min_loop_size_

◆ movemap_

◆ score_delta_

◆ scored_frag_cycle_ratio_

◆ scorefxn_

◆ short_frag_cycle_ratio_

◆ ss_info_

◆ vdw_delta_

◆ vdw_score_type_