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Rosetta
2020.11
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#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... | |
~LoopClosure () override | |
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 |
protocols::loops::loop_closure::ccd::LoopClosure::LoopClosure | ( | core::fragment::FragSetCOP | fragset, |
core::scoring::ScoreFunctionOP | scorefxn, | ||
Loop | loop_def, | ||
core::kinematics::MoveMapCOP | movemap | ||
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constructor: supply fragsets for fragment moves
References init(), set_cycles(), and temperature_.
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overridedefault |
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References set_cycles(), and temperature_.
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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(), protocols::mean_field::min(), movemap(), nr_fragments_, protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), protocols::hybridization::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().
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protectedvirtual |
save the loop-fragment in closure_frames_
Reimplemented in protocols::loops::loop_closure::ccd::ShortLoopClosure.
References closure_frame_.
Referenced by apply().
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inline |
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protectedvirtual |
References protocols::moves::TrialMover::apply(), bRampChainbreak_, ccd_mover_, cycles_, frag_mover_, mc_, ramp_chainbreak(), core::scoring::rg, and protocols::loops::loop_closure::ccd::tr().
Referenced by apply().
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protected |
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().
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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().
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inlineprotected |
References loop_.
Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), and apply().
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inline |
core::kinematics::MoveMapCOP protocols::loops::loop_closure::ccd::LoopClosure::movemap | ( | ) | const |
References movemap_.
Referenced by apply(), and protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().
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inline |
References nr_fragments_.
Referenced by protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), and set_nr_fragments().
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inline |
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protectedvirtual |
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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_, protocols::mean_field::max(), 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().
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References fragset_.
Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().
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References loop_.
Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().
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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().
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replace scorefxn
References init_mc(), scorefxn(), and scorefxn_.
Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().
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References temperature_.
Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().
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Referenced by init().
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Referenced by do_frag_cycles(), and ramp_chainbreak().
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Referenced by do_frag_cycles(), and init().
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Referenced by apply(), catch_fragment(), closure_fragments(), and init().
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Referenced by apply(), do_frag_cycles(), and set_cycles().
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Referenced by init_mc(), and ramp_chainbreak().
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Referenced by init_mc(), and ramp_chainbreak().
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Referenced by apply(), do_frag_cycles(), and init().
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Referenced by init(), and set_fragset().
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Referenced by apply(), init(), loop(), set_cycles(), and set_loop().
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Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), do_frag_cycles(), init_mc(), mc(), and ramp_chainbreak().
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Referenced by init(), movemap(), and set_movemap().
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Referenced by apply(), nr_fragments(), set_cycles(), and set_nr_fragments().
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Referenced by init(), init_mc(), ramp_chainbreak(), scorefxn(), and set_scorefxn().
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Referenced by init_mc(), LoopClosure(), and set_temperature().