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protocols::loophash::FastGapMover Class Reference

Not implemented! Mover class for closing gaps. More...

#include <FastGapMover.hh>

Inheritance diagram for protocols::loophash::FastGapMover:
Inheritance graph

Public Types

typedef core::Size Size
typedef core::Real Real
typedef core::pose::Pose Pose
- 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

Public Member Functions

 FastGapMover ()
moves::MoverOP clone () const override
 clone has to be overridden only if clone invocation is expected. More...
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
void apply (Pose &pose) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
FastGapMovermin_rms (core::Real const setting)
FastGapMovermax_rms (core::Real const setting)
FastGapMovernon_ideal (bool const setting)
- 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...
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 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...

Private Member Functions

void find_next_gap (Pose &pose, core::Size &idx, Real &gap_distance)

Private Attributes

LocalInserter_SimpleMinOP simple_inserter_
LoopHashLibraryOP lhlibrary_
LoopHashSamplerOP lhsampler_
core::Size min_loop_size_
core::Size max_loop_size_
core::Real max_rms_
core::Real min_rms_
bool non_ideal_

Additional Inherited Members

- 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 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...

Detailed Description

Not implemented! Mover class for closing gaps.

This Mover checks for any gaps using residue residue distances, then eats back at the chain surrounding it until LoopHash finds a fragment that fits in the space without changing the rest of pose too much. This mover depends on LoopHashSampler::close_gaps(), which is currently not implemented.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::loophash::FastGapMover::FastGapMover ( )

Member Function Documentation

void protocols::loophash::FastGapMover::apply ( Pose )
moves::MoverOP protocols::loophash::FastGapMover::clone ( ) const

clone has to be overridden only if clone invocation is expected.

Reimplemented from protocols::moves::Mover.

void protocols::loophash::FastGapMover::find_next_gap ( Pose pose,
core::Size idx,
Real gap_distance 
moves::MoverOP protocols::loophash::FastGapMover::fresh_instance ( ) const

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

string protocols::loophash::FastGapMover::get_name ( ) const

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

Implements protocols::moves::Mover.

FastGapMover& protocols::loophash::FastGapMover::max_rms ( core::Real const  setting)

References max_rms_.

FastGapMover& protocols::loophash::FastGapMover::min_rms ( core::Real const  setting)

References min_rms_.

FastGapMover& protocols::loophash::FastGapMover::non_ideal ( bool const  setting)

References non_ideal_.

Member Data Documentation

LoopHashLibraryOP protocols::loophash::FastGapMover::lhlibrary_

Referenced by FastGapMover().

LoopHashSamplerOP protocols::loophash::FastGapMover::lhsampler_

Referenced by apply(), and FastGapMover().

core::Size protocols::loophash::FastGapMover::max_loop_size_

Referenced by apply(), and FastGapMover().

core::Real protocols::loophash::FastGapMover::max_rms_

Referenced by apply(), and max_rms().

core::Size protocols::loophash::FastGapMover::min_loop_size_

Referenced by apply(), and FastGapMover().

core::Real protocols::loophash::FastGapMover::min_rms_

Referenced by apply(), and min_rms().

bool protocols::loophash::FastGapMover::non_ideal_

Referenced by apply(), and non_ideal().

LocalInserter_SimpleMinOP protocols::loophash::FastGapMover::simple_inserter_

Referenced by FastGapMover().

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