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Rosetta
2020.50
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#include <WidthFirstSlidingWindowLoopClosure.hh>
Public Member Functions | |
WidthFirstSlidingWindowLoopClosure (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn, core::kinematics::MoveMapCOP movemap) | |
constructor: supply fragsets for fragment moves More... | |
WidthFirstSlidingWindowLoopClosure () | |
void | sample_loops (core::pose::Pose &more_cut, core::pose::Pose &less_cut) override |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
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SlidingWindowLoopClosure (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn, core::kinematics::MoveMapCOP movemap) | |
constructor: supply fragsets for fragment moves More... | |
SlidingWindowLoopClosure () | |
~SlidingWindowLoopClosure () override | |
virtual void | apply (core::pose::Pose &more_cut, core::pose::Pose &less_cut) |
virtual void | select_final_loop (core::pose::Pose &more_cut, core::pose::Pose &less_cut) |
void | apply (core::pose::Pose &more_cut) override |
Main Method. More... | |
core::fragment::FragSetCOP | closure_fragments () const |
void | keep_fragments (bool setting=true) |
void | output_debug_structure (core::pose::Pose &pose, std::string prefix) |
core::kinematics::MoveMap const & | movemap () const |
void | movemap (core::kinematics::MoveMapCOP movemap) |
core::scoring::ScoreFunction const & | scorefxn () const |
void | scorefxn (core::scoring::ScoreFunctionOP sfxn) |
void | fragments (core::fragment::FragSetCOP frags) |
void | scored_frag_cycle_ratio (core::Real setting) |
void | short_frag_cycle_ratio (core::Real setting) |
void | set_bIdealLoopClosing (bool setting) |
bool | bIdealLoopClosing () const |
void | set_chainbreak_max (core::Real setting) |
void | set_evaluation (evaluation::MetaPoseEvaluatorOP ev) |
void | set_loop (Loop const &loop_in) |
Loop | determine_loop (core::pose::Pose const &more_cut, core::pose::Pose &less_cut) |
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Mover () | |
virtual MoverOP | create () |
MoverCOP | get_self_ptr () const |
MoverOP | get_self_ptr () |
MoverCAP | get_self_weak_ptr () const |
MoverAP | get_self_weak_ptr () |
Mover (std::string const &type_name) | |
sets the type for a mover; name_ has been removed (2010/05/14) More... | |
virtual void | test_move (Pose &pose) |
: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
virtual MoverOP | clone () const |
Return a clone of the Mover object. More... | |
virtual bool | reinitialize_for_each_job () const |
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
virtual bool | reinitialize_for_new_input () const |
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
virtual MoverOP | fresh_instance () const |
Generates a new Mover object freshly created with the default ctor. More... | |
MoverStatus | get_last_move_status () const |
end parser interface, start Job Distributor interface///////////// More... | |
void | reset_status () |
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
virtual core::pose::PoseOP | get_additional_output () |
Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
void | set_type (std::string const &setting) |
Set the 'type' string. More... | |
std::string | get_type () const |
void | type (const std::string &type_in) |
Set the 'type' string. More... | |
std::string const & | type () const |
Get the set 'type' string. More... | |
virtual void | set_input_pose (PoseCOP pose) |
setter for poses contained for rms More... | |
virtual void | set_native_pose (PoseCOP pose) |
setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
PoseCOP | get_input_pose () const |
PoseCOP | get_native_pose () const |
virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
virtual void | set_current_tag (std::string const &new_tag) |
std::string | get_current_tag () const |
A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
virtual void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. More... | |
virtual core::Real | last_proposal_density_ratio () |
virtual void | clear_info () |
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
virtual Strings & | info () |
non-const accessor More... | |
virtual Strings const & | info () const |
const accessor More... | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
static void | register_options () |
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static void | setPoseExtraScore (core::pose::Pose &pose) |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
Protected Member Functions | |
void | set_defaults () |
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void | generate_window_list (core::Size loop_size, WindowList &window_list) const |
void | set_defaults () |
core::scoring::ScoreFunctionOP | setup_frag_scorefxn () |
core::Size | process_fragments (core::fragment::FrameList &frame_in, core::pose::Pose const &more_cut, core::pose::Pose const &loop_pose) |
process fragments for loop-closing prowess, keep track of best_fragment return nr_of new good_loops ( vdw criterion ) More... | |
bool | bQuickTest () const |
core::Real | filter_score (core::pose::Pose &pose) |
return the score used for filtering ( scorefxn_ + filter_cst_weight_ * filter_cst_ ) More... | |
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void | set_last_move_status (MoverStatus status) |
nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Private Types | |
typedef SlidingWindowLoopClosure | Parent |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
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typedef std::list< std::pair < core::Real, Loop > > | WindowList |
it will switch between different windows. If nothing good is found after one sweep of window sizes we bail out... (assuming that it is fruitless) if things look promising more sampling time is spend to find a good loop
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protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::WidthFirstSlidingWindowLoopClosure | ( | core::fragment::FragSetCOP | fragset, |
core::scoring::ScoreFunctionOP | scorefxn, | ||
core::kinematics::MoveMapCOP | movemap | ||
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constructor: supply fragsets for fragment moves
References set_defaults().
protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::WidthFirstSlidingWindowLoopClosure | ( | ) |
References set_defaults().
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overridevirtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure.
Reimplemented in protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure.
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Reimplemented from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure.
References protocols::loops::add_single_cutpoint_variant(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::best_fragment_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::best_score_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bKeepFragments_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bQuickTest(), protocols::loops::loop_closure::ccd::LoopClosure::closure_fragments(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::closure_fragments_, protocols::evaluation::evaluate_pose(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::evaluator_, core::pose::Pose::fold_tree(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragset_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), give_up_, core::fragment::FragID::is_valid(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::loop_, protocols::mean_field::max(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::max_loop_size_, protocols::mean_field::min(), min_breakout_fast_loops_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_breakout_good_loops_, min_fast_loops_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_good_loops_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_loop_size_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap_, protocols::loops::loop_closure::ccd::LoopClosure::nr_fragments(), nr_scored_fragments_, nr_scored_sampling_passes_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::loops::loop_closure::ccd::LoopClosure::ramp_chainbreak(), protocols::loops::loop_closure::ccd::REALLY_BAD_SCORE(), protocols::loops::remove_cutpoint_variants(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::score_delta_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scored_frag_cycle_ratio_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn_, protocols::loops::loop_closure::ccd::LoopClosure::set_cycles(), protocols::loops::loop_closure::ccd::LoopClosure::set_nr_fragments(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setup_frag_scorefxn(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio_, protocols::loops::Loop::size(), protocols::loops::Loop::start(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::success(), core::id::to_string(), protocols::loops::loop_closure::ccd::tr(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::vdw_delta_, and window_acceptance_ratio_.
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References protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::chainbreak_max_, give_up_, min_breakout_fast_loops_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_breakout_good_loops_, min_fast_loops_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_good_loops_, nr_scored_fragments_, nr_scored_sampling_passes_, protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_defaults(), protocols::loops::loop_closure::ccd::tr(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::vdw_delta_, and window_acceptance_ratio_.
Referenced by protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::set_defaults(), and WidthFirstSlidingWindowLoopClosure().
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Referenced by sample_loops(), and set_defaults().
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Referenced by sample_loops(), and set_defaults().
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Referenced by sample_loops(), and set_defaults().
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Referenced by sample_loops(), and set_defaults().
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Referenced by sample_loops(), and set_defaults().
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Referenced by sample_loops(), and set_defaults().