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Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
protocols::loops::loop_closure::ccd::LoopClosure Class Reference

#include <LoopClosure.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::LoopClosure:
Inheritance graph
[legend]

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::MonteCarlomc ()
 
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(), and temperature_.

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

core::fragment::FrameOP protocols::loops::loop_closure::ccd::LoopClosure::closure_fragments ( ) const
inline
void protocols::loops::loop_closure::ccd::LoopClosure::do_frag_cycles ( core::pose::Pose pose) const
protectedvirtual
void protocols::loops::loop_closure::ccd::LoopClosure::init ( void  )
protected
void protocols::loops::loop_closure::ccd::LoopClosure::init_mc ( )
protected
Loop const& protocols::loops::loop_closure::ccd::LoopClosure::loop ( ) const
inlineprotected
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
core::Size protocols::loops::loop_closure::ccd::LoopClosure::nr_fragments ( ) const
inline
void protocols::loops::loop_closure::ccd::LoopClosure::ramp_chainbreak ( bool  setting = true)
inline
void protocols::loops::loop_closure::ccd::LoopClosure::ramp_chainbreak ( core::Size  iter,
core::Size  total 
) const
protectedvirtual
core::scoring::ScoreFunction const& protocols::loops::loop_closure::ccd::LoopClosure::scorefxn ( )
inline
void protocols::loops::loop_closure::ccd::LoopClosure::set_cycles ( core::Real  cycle_ratio = 1.0)
void protocols::loops::loop_closure::ccd::LoopClosure::set_fragset ( core::fragment::FragSetCOP  frags)
protected
void protocols::loops::loop_closure::ccd::LoopClosure::set_loop ( Loop const &  loop_in)
inlineprotected
void protocols::loops::loop_closure::ccd::LoopClosure::set_movemap ( core::kinematics::MoveMapCOP  mm)
protected
void protocols::loops::loop_closure::ccd::LoopClosure::set_nr_fragments ( core::Size  nr_fragments = 100)
void protocols::loops::loop_closure::ccd::LoopClosure::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)
protected
void protocols::loops::loop_closure::ccd::LoopClosure::set_temperature ( core::Real  temperature)
inlineprotected

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
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
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
core::scoring::ScoreFunctionOP protocols::loops::loop_closure::ccd::LoopClosure::scorefxn_
protected
core::Real protocols::loops::loop_closure::ccd::LoopClosure::temperature_
protected

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