#include <LoopClosure.hh>

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

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

	~LoopClosure () override

virtual bool	apply (core::pose::Pose const &pose)

core::fragment::FrameOP	closure_fragments () const

core::kinematics::MoveMapCOP	movemap () const

moves::MonteCarlo &	mc ()

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

void	set_cycles (core::Real cycle_ratio=1.0)

void	set_nr_fragments (core::Size nr_fragments=100)

core::Size	nr_fragments () const

void	ramp_chainbreak (bool setting=true)

Protected Member Functions
	LoopClosure ()

void	init ()

virtual void	do_frag_cycles (core::pose::Pose &pose) const

virtual void	catch_fragment (core::pose::Pose const &pose)
	save the loop-fragment in closure_frames_ More...

void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
	replace scorefxn More...

void	set_loop (Loop const &loop_in)

Loop const &	loop () const

void	init_mc ()

void	set_movemap (core::kinematics::MoveMapCOP mm)

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

void	set_temperature (core::Real temperature)

virtual void	ramp_chainbreak (core::Size iter, core::Size total) const

Constructor & Destructor Documentation

◆ LoopClosure() [1/2]

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

constructor: supply fragsets for fragment moves

References init(), set_cycles(), and temperature_.

◆ ~LoopClosure()

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

overridedefault

◆ LoopClosure() [2/2]

protocols::loops::loop_closure::ccd::LoopClosure::LoopClosure ( )

protected

References set_cycles(), and temperature_.

Member Function Documentation

◆ apply()

bool protocols::loops::loop_closure::ccd::LoopClosure::apply ( core::pose::Pose const & pose )

virtual

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

References protocols::loops::add_single_cutpoint_variant(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), catch_fragment(), closure_frame_, cycles_, protocols::loops::loop_closure::ccd::CCDLoopClosureMover::deviation(), do_frag_cycles(), frag_mover_, loop(), loop_, mc(), protocols::mean_field::min(), movemap(), nr_fragments_, protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), protocols::hybridization::score, protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::success(), and protocols::loops::loop_closure::ccd::tr().

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

◆ catch_fragment()

void protocols::loops::loop_closure::ccd::LoopClosure::catch_fragment ( core::pose::Pose const & pose )

protectedvirtual

save the loop-fragment in closure_frames_

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

References closure_frame_.

Referenced by apply().

◆ closure_fragments()

core::fragment::FrameOP protocols::loops::loop_closure::ccd::LoopClosure::closure_fragments ( ) const

inline

References closure_frame_.

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

◆ do_frag_cycles()

void protocols::loops::loop_closure::ccd::LoopClosure::do_frag_cycles ( core::pose::Pose & pose ) const

protectedvirtual

References protocols::moves::TrialMover::apply(), bRampChainbreak_, ccd_mover_, cycles_, frag_mover_, mc_, ramp_chainbreak(), core::scoring::rg, and protocols::loops::loop_closure::ccd::tr().

Referenced by apply().

◆ init()

void protocols::loops::loop_closure::ccd::LoopClosure::init ( void )

protected

References bEnableCcdMoves_, ccd_mover_, closure_frame_, frag_mover_, fragset_, init_mc(), loop_, movemap_, scorefxn_, set_movemap(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by LoopClosure(), and protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().

◆ init_mc()

void protocols::loops::loop_closure::ccd::LoopClosure::init_mc ( )

protected

References final_weight_linear_chainbreak_, final_weight_overlap_chainbreak_, core::scoring::linear_chainbreak, mc_, core::scoring::overlap_chainbreak, scorefxn_, and temperature_.

Referenced by init(), and set_scorefxn().

◆ loop()

Loop const& protocols::loops::loop_closure::ccd::LoopClosure::loop ( ) const

inlineprotected

References loop_.

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

◆ mc()

moves::MonteCarlo& protocols::loops::loop_closure::ccd::LoopClosure::mc ( )

inline

References mc_.

Referenced by apply().

◆ movemap()

core::kinematics::MoveMapCOP protocols::loops::loop_closure::ccd::LoopClosure::movemap ( ) const

References movemap_.

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

◆ nr_fragments()

core::Size protocols::loops::loop_closure::ccd::LoopClosure::nr_fragments ( ) const

inline

References nr_fragments_.

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

◆ ramp_chainbreak() [1/2]

void protocols::loops::loop_closure::ccd::LoopClosure::ramp_chainbreak ( bool setting = true )

inline

References bRampChainbreak_.

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

◆ ramp_chainbreak() [2/2]

void protocols::loops::loop_closure::ccd::LoopClosure::ramp_chainbreak	(	core::Size	iter,
		core::Size	total
	)		const

protectedvirtual

References final_weight_linear_chainbreak_, final_weight_overlap_chainbreak_, core::scoring::linear_chainbreak, mc_, core::scoring::overlap_chainbreak, scorefxn_, and protocols::analysis::total.

◆ scorefxn()

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

inline

References scorefxn_.

Referenced by set_scorefxn(), and protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().

◆ set_cycles()

void protocols::loops::loop_closure::ccd::LoopClosure::set_cycles ( core::Real cycle_ratio = 1.0 )

References cycles_, loop_, protocols::mean_field::max(), nr_fragments_, and protocols::loops::Loop::size().

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

◆ set_fragset()

void protocols::loops::loop_closure::ccd::LoopClosure::set_fragset ( core::fragment::FragSetCOP frags )

protected

References fragset_.

Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().

◆ set_loop()

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

inlineprotected

References loop_.

Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().

◆ set_movemap()

void protocols::loops::loop_closure::ccd::LoopClosure::set_movemap ( core::kinematics::MoveMapCOP mm )

protected

References movemap_.

Referenced by init(), and protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().

◆ set_nr_fragments()

void protocols::loops::loop_closure::ccd::LoopClosure::set_nr_fragments ( core::Size nr_fragments = 100 )

References nr_fragments(), and nr_fragments_.

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

◆ set_scorefxn()

void protocols::loops::loop_closure::ccd::LoopClosure::set_scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

protected

replace scorefxn

References init_mc(), scorefxn(), and scorefxn_.

Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().

◆ set_temperature()

void protocols::loops::loop_closure::ccd::LoopClosure::set_temperature ( core::Real temperature )

inlineprotected

References temperature_.

Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().

Member Data Documentation

◆ bEnableCcdMoves_

bool protocols::loops::loop_closure::ccd::LoopClosure::bEnableCcdMoves_

protected

Referenced by init().

◆ bRampChainbreak_

bool protocols::loops::loop_closure::ccd::LoopClosure::bRampChainbreak_

protected

Referenced by do_frag_cycles(), and ramp_chainbreak().

◆ ccd_mover_

moves::MoverOP protocols::loops::loop_closure::ccd::LoopClosure::ccd_mover_

protected

Referenced by do_frag_cycles(), and init().

◆ closure_frame_

core::fragment::FrameOP protocols::loops::loop_closure::ccd::LoopClosure::closure_frame_

protected

Referenced by apply(), catch_fragment(), closure_fragments(), and init().

◆ cycles_

core::Size protocols::loops::loop_closure::ccd::LoopClosure::cycles_

protected

Referenced by apply(), do_frag_cycles(), and set_cycles().

◆ final_weight_linear_chainbreak_

core::Real protocols::loops::loop_closure::ccd::LoopClosure::final_weight_linear_chainbreak_

protected

Referenced by init_mc(), and ramp_chainbreak().

◆ final_weight_overlap_chainbreak_

core::Real protocols::loops::loop_closure::ccd::LoopClosure::final_weight_overlap_chainbreak_

protected

Referenced by init_mc(), and ramp_chainbreak().

◆ frag_mover_

simple_moves::FragmentMoverOP protocols::loops::loop_closure::ccd::LoopClosure::frag_mover_

protected

Referenced by apply(), do_frag_cycles(), and init().

◆ fragset_

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

protected

Referenced by init(), and set_fragset().

◆ loop_

Loop protocols::loops::loop_closure::ccd::LoopClosure::loop_

protected

Referenced by apply(), init(), loop(), set_cycles(), and set_loop().

◆ mc_

moves::MonteCarloOP protocols::loops::loop_closure::ccd::LoopClosure::mc_

protected

Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), do_frag_cycles(), init_mc(), mc(), and ramp_chainbreak().

◆ movemap_

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

protected

Referenced by init(), movemap(), and set_movemap().

◆ nr_fragments_

core::Size protocols::loops::loop_closure::ccd::LoopClosure::nr_fragments_

protected

Referenced by apply(), nr_fragments(), set_cycles(), and set_nr_fragments().

◆ scorefxn_

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

protected

Referenced by init(), init_mc(), ramp_chainbreak(), scorefxn(), and set_scorefxn().

◆ temperature_

core::Real protocols::loops::loop_closure::ccd::LoopClosure::temperature_

protected

Referenced by init_mc(), LoopClosure(), and set_temperature().

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

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

Protected Attributes
Loop	loop_

core::scoring::ScoreFunctionOP	scorefxn_

core::Real	temperature_

core::kinematics::MoveMapCOP	movemap_

moves::MonteCarloOP	mc_

core::fragment::FrameOP	closure_frame_

core::Size	nr_fragments_

core::Size	cycles_

simple_moves::FragmentMoverOP	frag_mover_

moves::MoverOP	ccd_mover_

core::fragment::FragSetCOP	fragset_

bool	bEnableCcdMoves_

bool	bRampChainbreak_

core::Real	final_weight_linear_chainbreak_

core::Real	final_weight_overlap_chainbreak_

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ LoopClosure() [1/2]

◆ ~LoopClosure()

◆ LoopClosure() [2/2]

Member Function Documentation

◆ apply()

◆ catch_fragment()

◆ closure_fragments()

◆ do_frag_cycles()

◆ init()

◆ init_mc()

◆ loop()

◆ mc()

◆ movemap()

◆ nr_fragments()

◆ ramp_chainbreak() [1/2]

◆ ramp_chainbreak() [2/2]

◆ scorefxn()

◆ set_cycles()

◆ set_fragset()

◆ set_loop()

◆ set_movemap()

◆ set_nr_fragments()

◆ set_scorefxn()

◆ set_temperature()

Member Data Documentation

◆ bEnableCcdMoves_

◆ bRampChainbreak_

◆ ccd_mover_

◆ closure_frame_

◆ cycles_

◆ final_weight_linear_chainbreak_

◆ final_weight_overlap_chainbreak_

◆ frag_mover_

◆ fragset_

◆ loop_

◆ mc_

◆ movemap_

◆ nr_fragments_

◆ scorefxn_

◆ temperature_