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

More...

#include <WidthFirstSlidingWindowLoopClosure.hh>

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

List of all members.

Public Member Functions

 WidthFirstSlidingWindowLoopClosure (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn, core::kinematics::MoveMapCOP movemap)
 constructor: supply fragsets for fragment moves
 WidthFirstSlidingWindowLoopClosure ()
virtual void sample_loops (core::pose::Pose &more_cut, core::pose::Pose &less_cut)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.

Static Public Member Functions

static void register_options ()
 overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method.

Protected Member Functions

void set_defaults ()

Protected Attributes

core::Real window_acceptance_ratio_
core::Size nr_scored_sampling_passes_
core::Size min_fast_loops_
core::Size min_breakout_fast_loops_
core::Size nr_scored_fragments_
core::Size give_up_

Detailed Description

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


Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::WidthFirstSlidingWindowLoopClosure ( core::fragment::FragSetCOP  fragset,
core::scoring::ScoreFunctionOP  scorefxn,
core::kinematics::MoveMapCOP  movemap 
)

constructor: supply fragsets for fragment moves

References set_defaults().

protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::WidthFirstSlidingWindowLoopClosure ( )

References set_defaults().


Member Function Documentation

std::string protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::get_name ( ) const [virtual]

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.

void protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::register_options ( ) [static]

overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure.

void protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops ( core::pose::Pose more_cut,
core::pose::Pose less_cut 
) [virtual]

Reimplemented from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure.

References protocols::loops::add_single_cutpoint_variant(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::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::loops::loop_closure::ccd::SlidingWindowLoopClosure::max_loop_size_, 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(), protocols::loops::loop_closure::ccd::tr(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::vdw_delta_, and window_acceptance_ratio_.

void protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::set_defaults ( ) [protected]

Member Data Documentation

Referenced by sample_loops(), and set_defaults().

Referenced by sample_loops(), and set_defaults().

Referenced by sample_loops(), and set_defaults().

Referenced by sample_loops(), and set_defaults().

Referenced by sample_loops(), and set_defaults().

Referenced by sample_loops(), and set_defaults().


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines