protocols::loops::loop_closure::ccd::LoopClosure Class Reference

#include <LoopClosure.hh>

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...
virtual	~LoopClosure ()
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

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_

Constructor & Destructor Documentation

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(), size(), and temperature_.

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

virtual

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

protected

References set_cycles(), and temperature_.

Member Function Documentation

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(), movemap(), nr_fragments_, core::fragment::Frame::nr_frags(), protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), 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::WidthFirstSlidingWindowLoopClosure::sample_loops(), and protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops().

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_, runtime_assert, and core::fragment::Frame::steal().

Referenced by apply().

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

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(), protocols::loops::loop_closure::ccd::RG, protocols::loops::loop_closure::ccd::tr, and numeric::random::RandomGenerator::uniform().

Referenced by apply().

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

protected

References bEnableCcdMoves_, ccd_mover_, closure_frame_, protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(), frag_mover_, fragset_, init_mc(), loop_, movemap_, runtime_assert, scorefxn_, core::kinematics::MoveMap::set_bb(), protocols::simple_moves::ClassicFragmentMover::set_check_ss(), 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().

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

protected

References final_weight_linear_chainbreak_, final_weight_overlap_chainbreak_, mc_, protocols::forge::methods::overlap_chainbreak(), scorefxn_, and temperature_.

Referenced by init(), and set_scorefxn().

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

inlineprotected

References loop_.

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

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

inline

References mc_.

Referenced by apply().

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

(

)

const

References movemap_.

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

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().

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

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_, mc_, protocols::forge::methods::overlap_chainbreak(), runtime_assert, protocols::moves::MonteCarlo::score_function(), and 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().

void protocols::loops::loop_closure::ccd::LoopClosure::set_cycles

(

core::Real

cycle_ratio = 1.0

)

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

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

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().

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().

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().

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().

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().

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

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

protected

Referenced by init().

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

protected

Referenced by do_frag_cycles(), and ramp_chainbreak().

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

protected

Referenced by do_frag_cycles(), and init().

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

protected

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

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

protected

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

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

protected

Referenced by init_mc(), and ramp_chainbreak().

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

protected

Referenced by init_mc(), and ramp_chainbreak().

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

protected

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

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

protected

Referenced by init(), and set_fragset().

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

protected

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

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().

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

protected

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

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

protected

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

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

protected

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

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

protected

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

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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