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

#include <SlidingWindowLoopClosure.hh>

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List of all members.

Public Member Functions

 SlidingWindowLoopClosure (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn, core::kinematics::MoveMapCOP movemap)
 constructor: supply fragsets for fragment moves
 SlidingWindowLoopClosure ()
 ~SlidingWindowLoopClosure ()
virtual void apply (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.
virtual void sample_loops (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)
virtual void apply (core::pose::Pose &more_cut)
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)

Static Public Member Functions

static void setPoseExtraScores (core::pose::Pose &pose)

Protected Types

typedef std::list< std::pair
< core::Real, Loop > > 
WindowList

Protected Member Functions

void generate_window_list (Size loop_size, WindowList &window_list) const
void set_defaults ()
void setup_frag_scorefxn (core::scoring::ScoreFunction &scorefxn)
Size process_fragments (core::fragment::FrameList &frame_in, core::pose::Pose const &more_cut, core::pose::Pose const &loop_pose)
bool bQuickTest () const
core::Real filter_score (core::pose::Pose &pose)
 return the score used for filtering ( scorefxn_ + filter_cst_weight_ * filter_cst_ )

Protected Attributes

Loop loop_
core::scoring::ScoreFunctionOP scorefxn_
core::kinematics::MoveMapCOP movemap_
core::fragment::FragSetCOP fragset_
core::fragment::SecondaryStructureOP ss_info_
core::Size min_loop_size_
core::Size max_loop_size_
core::Size min_good_loops_
core::Size min_breakout_good_loops_
core::Real vdw_delta_
core::Real chainbreak_max_
core::Real score_delta_
core::Real scored_frag_cycle_ratio_
core::Real short_frag_cycle_ratio_
core::scoring::ScoreType vdw_score_type_
bool bKeepFragments_
core::fragment::OrderedFragSetOP closure_fragments_
core::Real best_score_
core::fragment::FragID best_fragment_
bool bQuickTest_
bool bIdealLoopClosing_
evaluation::MetaPoseEvaluatorOP evaluator_
constraints_additional::ConstraintEvaluatorOP filter_cst_
core::Real filter_cst_weight_

Member Typedef Documentation


Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::SlidingWindowLoopClosure ( 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::SlidingWindowLoopClosure::SlidingWindowLoopClosure ( )

References set_defaults().

protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::~SlidingWindowLoopClosure ( )

Member Function Documentation

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

Implements protocols::moves::Mover.

References apply(), and bIdealLoopClosing().

bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bIdealLoopClosing ( ) const [inline]

References bIdealLoopClosing_.

Referenced by apply(), and process_fragments().

bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bQuickTest ( ) const [inline, protected]
core::fragment::FragSetCOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::closure_fragments ( ) const [inline]
Loop protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop ( core::pose::Pose const &  more_cut,
core::pose::Pose less_cut 
)
Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::filter_score ( core::pose::Pose pose) [protected]

return the score used for filtering ( scorefxn_ + filter_cst_weight_ * filter_cst_ )

References filter_cst_, filter_cst_weight_, and scorefxn_.

Referenced by process_fragments().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragments ( core::fragment::FragSetCOP  frags) [inline]

References fragset_, and ss_info_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list ( Size  loop_size,
WindowList window_list 
) const [protected]
std::string protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::get_name ( ) const [virtual]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::keep_fragments ( bool  setting = true) [inline]
core::kinematics::MoveMap const& protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap ( ) const [inline]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap ( core::kinematics::MoveMapCOP  movemap)

References movemap(), and movemap_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::output_debug_structure ( core::pose::Pose pose,
std::string  prefix 
)
Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments ( core::fragment::FrameList frame_in,
core::pose::Pose const &  more_cut,
core::pose::Pose const &  loop_pose 
) [protected]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops ( core::pose::Pose more_cut,
core::pose::Pose less_cut 
) [virtual]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scored_frag_cycle_ratio ( core::Real  setting) [inline]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn ( core::scoring::ScoreFunctionOP  sfxn) [inline]

References scorefxn_.

core::scoring::ScoreFunction const& protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn ( ) const [inline]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::select_final_loop ( core::pose::Pose more_cut,
core::pose::Pose less_cut 
) [virtual]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_bIdealLoopClosing ( bool  setting) [inline]

References bIdealLoopClosing_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_chainbreak_max ( core::Real  setting) [inline]

References chainbreak_max_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_defaults ( ) [protected]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_evaluation ( evaluation::MetaPoseEvaluatorOP  ev) [inline]

References evaluator_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_loop ( Loop const &  loop_in) [inline]

References loop_.

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setPoseExtraScores ( core::pose::Pose pose) [static]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setup_frag_scorefxn ( core::scoring::ScoreFunction scorefxn) [protected]
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio ( core::Real  setting) [inline]

Member Data Documentation

Referenced by bQuickTest(), and set_defaults().

Referenced by fragments(), and generate_window_list().

Referenced by process_fragments(), and set_defaults().


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