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protocols::rna::denovo::movers::RNA_Relaxer Class Reference

The RNA de novo structure modeling protocol. More...

#include <RNA_Relaxer.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNA_Relaxer:
Inheritance graph

Public Member Functions

 RNA_Relaxer (RNA_FragmentMoverOP rna_fragment_mover, RNA_MinimizerOP rna_minimizer)
 Construct the protocol object given the RNA fragment library to use. More...
 ~RNA_Relaxer () override
void apply (core::pose::Pose &pose) override
 Clone this object. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void simple_rmsd_cutoff_relax (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 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...

Private Member Functions

void make_fragment_moves (core::pose::Pose &pose)
void find_fragment_by_simple_rmsd_cutoff (core::pose::Pose &pose)
void lores_monte_carlo (core::pose::Pose &pose)

Private Attributes

RNA_FragmentMoverOP rna_fragment_mover_
RNA_MinimizerOP rna_minimizer_
core::Size const relax_cycles_
core::Size const max_frag_size_
core::Size const num_find_fragment_tries_
core::Real const rmsd_min_cutoff_
core::Real const rmsd_max_cutoff_
bool simple_rmsd_cutoff_relax_

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
- 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

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::rna::denovo::movers::RNA_Relaxer::RNA_Relaxer ( RNA_FragmentMoverOP  rna_fragment_mover,
RNA_MinimizerOP  rna_minimizer 

Construct the protocol object given the RNA fragment library to use.

protocols::rna::denovo::movers::RNA_Relaxer::~RNA_Relaxer ( )

Member Function Documentation

void protocols::rna::denovo::movers::RNA_Relaxer::apply ( core::pose::Pose pose)
void protocols::rna::denovo::movers::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff ( core::pose::Pose pose)
std::string protocols::rna::denovo::movers::RNA_Relaxer::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::rna::denovo::movers::RNA_Relaxer::lores_monte_carlo ( core::pose::Pose pose)
void protocols::rna::denovo::movers::RNA_Relaxer::make_fragment_moves ( core::pose::Pose pose)
void protocols::rna::denovo::movers::RNA_Relaxer::simple_rmsd_cutoff_relax ( bool const  setting)

Member Data Documentation

core::Size const protocols::rna::denovo::movers::RNA_Relaxer::max_frag_size_
core::Size const protocols::rna::denovo::movers::RNA_Relaxer::num_find_fragment_tries_
core::Size const protocols::rna::denovo::movers::RNA_Relaxer::relax_cycles_

Referenced by apply().

core::Real const protocols::rna::denovo::movers::RNA_Relaxer::rmsd_max_cutoff_
core::Real const protocols::rna::denovo::movers::RNA_Relaxer::rmsd_min_cutoff_
RNA_FragmentMoverOP protocols::rna::denovo::movers::RNA_Relaxer::rna_fragment_mover_
RNA_MinimizerOP protocols::rna::denovo::movers::RNA_Relaxer::rna_minimizer_

Referenced by apply().

bool protocols::rna::denovo::movers::RNA_Relaxer::simple_rmsd_cutoff_relax_

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