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protocols::pose_length_moves::AnalyzeLoopModeling Class Reference

#include <AnalyzeLoopModeling.hh>

Inheritance diagram for protocols::pose_length_moves::AnalyzeLoopModeling:
Inheritance graph

Public Member Functions

 AnalyzeLoopModeling ()
core::Real rmsd_between_coordinates (std::vector< numeric::xyzVector< core::Real > > fragCoordinates, std::vector< numeric::xyzVector< core::Real > > coordinates)
core::Real get_loop_rmsd (core::pose::Pose native_pose, core::pose::Pose designed_pose, core::Size loopStart, core::Size loopEnd)
core::Size get_valid_resid (int resid, core::pose::Pose const pose)
core::Real generate_lookback_rmsd (core::pose::Pose pose, core::Size position)
void apply (Pose &pose) override
 Main Method. More...
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
- 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 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
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 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 std::string mover_name ()
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
- 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...

Private Member Functions

protocols::loops::Loops get_loops (core::pose::Pose const &pose)

Private Attributes

core::Size loopLengthRangeLow_
core::Size loopLengthRangeHigh_

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
- 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...

Constructor & Destructor Documentation

protocols::pose_length_moves::AnalyzeLoopModeling::AnalyzeLoopModeling ( )

Member Function Documentation

void protocols::pose_length_moves::AnalyzeLoopModeling::apply ( Pose )
moves::MoverOP protocols::pose_length_moves::AnalyzeLoopModeling::clone ( ) const

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

Real protocols::pose_length_moves::AnalyzeLoopModeling::generate_lookback_rmsd ( core::pose::Pose  pose,
core::Size  position 
Real protocols::pose_length_moves::AnalyzeLoopModeling::get_loop_rmsd ( core::pose::Pose  native_pose,
core::pose::Pose  designed_pose,
core::Size  loopStart,
core::Size  loopEnd 
protocols::loops::Loops protocols::pose_length_moves::AnalyzeLoopModeling::get_loops ( core::pose::Pose const &  pose)
std::string protocols::pose_length_moves::AnalyzeLoopModeling::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

Size protocols::pose_length_moves::AnalyzeLoopModeling::get_valid_resid ( int  resid,
core::pose::Pose const  pose 
std::string protocols::pose_length_moves::AnalyzeLoopModeling::mover_name ( )
void protocols::pose_length_moves::AnalyzeLoopModeling::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References protocols::indexed_structure_store::SSHashedFragmentStore::init_SS_stub_HashedFragmentStore(), loopLengthRangeHigh_, loopLengthRangeLow_, protocols::indexed_structure_store::SSHashedFragmentStore::set_threshold_distance(), SSHashedFragmentStore_, and protocols::TR().

void protocols::pose_length_moves::AnalyzeLoopModeling::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
Real protocols::pose_length_moves::AnalyzeLoopModeling::rmsd_between_coordinates ( std::vector< numeric::xyzVector< core::Real > >  fragCoordinates,
std::vector< numeric::xyzVector< core::Real > >  coordinates 

Referenced by get_loop_rmsd().

Member Data Documentation

core::Size protocols::pose_length_moves::AnalyzeLoopModeling::loopLengthRangeHigh_

Referenced by apply(), and parse_my_tag().

core::Size protocols::pose_length_moves::AnalyzeLoopModeling::loopLengthRangeLow_

Referenced by apply(), and parse_my_tag().

protocols::indexed_structure_store::SSHashedFragmentStore* protocols::pose_length_moves::AnalyzeLoopModeling::SSHashedFragmentStore_

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