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protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure Class Reference

#include <SlidingWindowLoopClosure.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure:
Inheritance graph
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Public Member Functions

 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)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
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)
 
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)
 
- Public Member Functions inherited from protocols::moves::Mover
 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void setPoseExtraScore (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. More...
 

Protected Types

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

Protected Member Functions

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...
 
- Protected Member Functions inherited from protocols::moves::Mover
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...
 

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_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

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 ( )
overridedefault

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 )
overridevirtual

Main Method.

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
inlineprotected
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_, protocols::hybridization::score, and scorefxn_.

Referenced by process_fragments().

void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragments ( core::fragment::FragSetCOP  frags)
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list ( core::Size  loop_size,
WindowList window_list 
) const
protected
std::string protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::get_name ( ) const
overridevirtual
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
core::scoring::ScoreFunction const& protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn ( ) const
inline
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn ( core::scoring::ScoreFunctionOP  sfxn)
inline

References scorefxn_.

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)
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setPoseExtraScore ( core::pose::Pose pose)
static
core::scoring::ScoreFunctionOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setup_frag_scorefxn ( )
protected
void protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio ( core::Real  setting)
inline

Member Data Documentation

core::fragment::FragID protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::best_fragment_
protected
core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::best_score_
protected
bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bIdealLoopClosing_
protected
bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bKeepFragments_
protected
bool protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::bQuickTest_
protected

Referenced by bQuickTest(), and set_defaults().

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::chainbreak_max_
protected
core::fragment::OrderedFragSetOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::closure_fragments_
protected
evaluation::MetaPoseEvaluatorOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::evaluator_
protected
constraints_additional::ConstraintEvaluatorOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::filter_cst_
protected
core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::filter_cst_weight_
protected
core::fragment::FragSetCOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragset_
protected
Loop protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::loop_
protected
core::Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::max_loop_size_
protected
core::Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_breakout_good_loops_
protected
core::Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_good_loops_
protected
core::Size protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::min_loop_size_
protected
core::kinematics::MoveMapCOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::movemap_
protected
core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::score_delta_
protected
core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scored_frag_cycle_ratio_
protected
core::scoring::ScoreFunctionOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::scorefxn_
protected
core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::short_frag_cycle_ratio_
protected
core::fragment::SecondaryStructureOP protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::ss_info_
protected

Referenced by fragments(), and generate_window_list().

core::Real protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::vdw_delta_
protected
core::scoring::ScoreType protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::vdw_score_type_
protected

Referenced by process_fragments(), and set_defaults().


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