protocols::loops::loop_closure::ccd::ShortLoopClosure Class Reference

#include <ShortLoopClosure.hh>

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

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

Public Member Functions
	ShortLoopClosure (core::fragment::FragSetCOP fragset, Loop loop_def, core::kinematics::MoveMapCOP movemap)
virtual bool	apply (core::pose::Pose const &pose)
virtual void	catch_fragment (core::pose::Pose const &short_pose)
	save the loop-fragment in closure_frames_ More...
Public Member Functions inherited from 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 More...
virtual	~LoopClosure ()
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)

Private Types
typedef LoopClosure	Parent

Private Attributes
Loop	orig_loop_

Additional Inherited Members
Protected Member Functions inherited from protocols::loops::loop_closure::ccd::LoopClosure
	LoopClosure ()
void	init ()
virtual void	do_frag_cycles (core::pose::Pose &pose) const
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 inherited from protocols::loops::loop_closure::ccd::LoopClosure
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_

Detailed Description

Definition at line 34 of file ShortLoopClosure.hh.

Member Typedef Documentation

typedef LoopClosure protocols::loops::loop_closure::ccd::ShortLoopClosure::Parent

private

Definition at line 35 of file ShortLoopClosure.hh.

Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure	(	core::fragment::FragSetCOP	fragset,
		Loop	loop_def,
		core::kinematics::MoveMapCOP	movemap
	)

Definition at line 81 of file ShortLoopClosure.cc.

References protocols::loops::Loop::cut(), protocols::loops::loop_closure::ccd::LoopClosure::init(), core::scoring::linear_chainbreak, protocols::loops::loop_closure::ccd::LoopClosure::movemap(), core::scoring::overlap_chainbreak, protocols::loops::loop_closure::ccd::LoopClosure::scorefxn(), protocols::loops::loop_closure::ccd::LoopClosure::set_fragset(), protocols::loops::loop_closure::ccd::LoopClosure::set_loop(), protocols::loops::loop_closure::ccd::LoopClosure::set_movemap(), protocols::loops::loop_closure::ccd::LoopClosure::set_scorefxn(), protocols::loops::loop_closure::ccd::LoopClosure::set_temperature(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::loops::loop_closure::ccd::tr().

Member Function Documentation

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

virtual

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

Definition at line 129 of file ShortLoopClosure.cc.

References protocols::loops::loop_closure::ccd::LoopClosure::apply(), core::chemical::CENTROID, core::pose::Pose::copy_segment(), core::pose::Pose::fold_tree(), protocols::loops::loop_closure::ccd::LoopClosure::loop(), core::pose::make_pose_from_sequence(), protocols::loops::loop_closure::ccd::LoopClosure::mc_, core::kinematics::FoldTree::new_jump(), orig_loop_, core::pose::Pose::sequence(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), and protocols::loops::loop_closure::ccd::tr().

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

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

virtual

save the loop-fragment in closure_frames_

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

Definition at line 151 of file ShortLoopClosure.cc.

References protocols::loops::loop_closure::ccd::LoopClosure::closure_fragments(), orig_loop_, and protocols::loops::Loop::start().

Member Data Documentation

Loop protocols::loops::loop_closure::ccd::ShortLoopClosure::orig_loop_

private

Definition at line 52 of file ShortLoopClosure.hh.

Referenced by apply(), and catch_fragment().

---

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

• src/protocols/loops/loop_closure/ccd/ShortLoopClosure.hh
• src/protocols/loops/loop_closure/ccd/ShortLoopClosure.cc