Rosetta 3.4
Public Member Functions | Protected Member Functions | Protected Attributes
protocols::loops::loop_closure::ccd::LoopClosure Class Reference

#include <LoopClosure.hh>

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List of all members.

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
 ~LoopClosure ()
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_
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 replace scorefxn
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 ( )
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) [protected, virtual]

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 [protected, virtual]
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 [inline, protected]
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 [protected, virtual]
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) [inline, protected]
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) [inline, protected]

Member Data Documentation

Referenced by init().

Referenced by do_frag_cycles(), and ramp_chainbreak().

Referenced by do_frag_cycles(), and init().

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

Referenced by init_mc(), and ramp_chainbreak().

Referenced by init_mc(), and ramp_chainbreak().

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

Referenced by init(), and set_fragset().

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

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


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