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protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure Class Reference

#include <FASelectSlidingWindowLoopClosure.hh>

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Public Member Functions

 FASelectSlidingWindowLoopClosure (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn, core::kinematics::MoveMapCOP movemap)
 constructor: supply fragsets for fragment moves More...
 
 FASelectSlidingWindowLoopClosure ()
 
 ~FASelectSlidingWindowLoopClosure ()
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_defaults ()
 
virtual void select_final_loop (core::pose::Pose &more_cut, core::pose::Pose &less_cut)
 
core::Real fascore (core::pose::Pose &fa_pose) const
 
void set_fullatom_pose (core::pose::Pose &fa_pose)
 
- Public Member Functions inherited from 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 More...
 
 WidthFirstSlidingWindowLoopClosure ()
 
virtual void sample_loops (core::pose::Pose &more_cut, core::pose::Pose &less_cut)
 
- Public Member Functions inherited from 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 More...
 
 SlidingWindowLoopClosure ()
 
 ~SlidingWindowLoopClosure ()
 
virtual void apply (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)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Static Public Member Functions

static void register_options ()
 
- Static Public Member Functions inherited from protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
static void register_options ()
 
- Static Public Member Functions inherited from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
static void setPoseExtraScores (core::pose::Pose &pose)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
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. More...
 

Private Types

typedef
WidthFirstSlidingWindowLoopClosure 
Parent
 

Private Attributes

core::pose::PoseOP fa_pose_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- Protected Types inherited from protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
typedef std::list< std::pair
< core::Real, Loop > > 
WindowList
 
- Protected Member Functions inherited from protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
void set_defaults ()
 
- Protected Attributes inherited from protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
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_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::FASelectSlidingWindowLoopClosure ( 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::FASelectSlidingWindowLoopClosure::FASelectSlidingWindowLoopClosure ( )

References set_defaults().

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

Member Function Documentation

core::Real protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore ( core::pose::Pose fa_pose) const
std::string protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::get_name ( ) const
virtual

Each derived class must specify its name. The class name.

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

void protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::register_options ( )
static
void protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop ( core::pose::Pose more_cut,
core::pose::Pose less_cut 
)
virtual
void protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::set_defaults ( )
void protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::set_fullatom_pose ( core::pose::Pose fa_pose)

References fa_pose_.

Member Data Documentation

core::pose::PoseOP protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fa_pose_
private

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