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

#include <LoopClosure.hh>

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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_
 

Detailed Description

Definition at line 64 of file LoopClosure.hh.

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

Definition at line 77 of file LoopClosure.cc.

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

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

Definition at line 141 of file LoopClosure.cc.

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

Definition at line 96 of file LoopClosure.cc.

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.

Definition at line 160 of file LoopClosure.cc.

References protocols::loops::add_single_cutpoint_variant(), protocols::loops::loop_closure::ccd::CcdLoopClosureMover::apply(), protocols::loops::loop_closure::ccd::CcdLoopClosureMover::backward_deviation(), catch_fragment(), closure_frame_, cycles_, do_frag_cycles(), protocols::loops::loop_closure::ccd::CcdLoopClosureMover::forward_deviation(), frag_mover_, loop(), loop_, mc(), movemap(), nr_fragments_, protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), 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.

Definition at line 235 of file LoopClosure.cc.

References closure_frame_.

Referenced by apply().

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

Definition at line 84 of file LoopClosure.hh.

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

Definition at line 218 of file LoopClosure.cc.

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

Referenced by apply().

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

Definition at line 114 of file LoopClosure.cc.

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().

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

Definition at line 152 of file LoopClosure.cc.

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

Definition at line 155 of file LoopClosure.hh.

References loop_.

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

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

Definition at line 97 of file LoopClosure.hh.

References mc_.

Referenced by apply().

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

Definition at line 108 of file LoopClosure.cc.

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

Definition at line 117 of file LoopClosure.hh.

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

Definition at line 121 of file LoopClosure.hh.

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

Definition at line 203 of file LoopClosure.cc.

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

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

Definition at line 106 of file LoopClosure.hh.

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)

Definition at line 143 of file LoopClosure.cc.

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

Definition at line 112 of file LoopClosure.cc.

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

Definition at line 151 of file LoopClosure.hh.

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

Definition at line 110 of file LoopClosure.cc.

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)

Definition at line 148 of file LoopClosure.cc.

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

Definition at line 241 of file LoopClosure.cc.

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

Definition at line 166 of file LoopClosure.hh.

References temperature_.

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

Member Data Documentation

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

Definition at line 196 of file LoopClosure.hh.

Referenced by init().

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

Definition at line 197 of file LoopClosure.hh.

Referenced by do_frag_cycles(), and ramp_chainbreak().

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

Definition at line 192 of file LoopClosure.hh.

Referenced by do_frag_cycles(), and init().

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

Definition at line 186 of file LoopClosure.hh.

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

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

Definition at line 189 of file LoopClosure.hh.

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

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

Definition at line 198 of file LoopClosure.hh.

Referenced by init_mc(), and ramp_chainbreak().

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

Definition at line 199 of file LoopClosure.hh.

Referenced by init_mc(), and ramp_chainbreak().

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

Definition at line 191 of file LoopClosure.hh.

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

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

Definition at line 194 of file LoopClosure.hh.

Referenced by init(), and set_fragset().

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

Definition at line 173 of file LoopClosure.hh.

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

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

Definition at line 184 of file LoopClosure.hh.

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

Definition at line 181 of file LoopClosure.hh.

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

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

Definition at line 188 of file LoopClosure.hh.

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

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

Definition at line 175 of file LoopClosure.hh.

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

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

Definition at line 178 of file LoopClosure.hh.

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

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