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protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker Class Reference

#include <RNA_ChainClosureChecker.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker:
Inheritance graph

Public Member Functions

 RNA_ChainClosureChecker (core::pose::Pose const &pose, core::Size const five_prime_res)
 ~RNA_ChainClosureChecker () override
void apply (core::pose::Pose &pose) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void set_reinitialize_CCD_torsions (bool const &setting)
void copy_CCD_torsions (core::pose::Pose &pose) const
void copy_CCD_torsions_general (core::pose::Pose &pose, core::Size const five_prime_res, core::Size const three_prime_res) const
bool check_loop_closed (core::pose::Pose const &pose)
bool chain_break_screening_general (core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, core::Size const five_)
bool check_screen ()
bool check_screen (core::pose::Pose &pose)
core::pose::Posepose ()
core::Size const & five_prime_res () const
- 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 Attributes

core::pose::Pose chain_break_screening_pose_
core::Size const five_prime_res_
bool reinitialize_CCD_torsions_
bool verbose_
core::scoring::ScoreFunctionOP chain_break_scorefxn_
StepWiseRNA_CountStruct count_data_

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...

Constructor & Destructor Documentation

protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::RNA_ChainClosureChecker ( core::pose::Pose const &  pose,
core::Size const  five_prime_res 
protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::~RNA_ChainClosureChecker ( )

Member Function Documentation

void protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::apply ( core::pose::Pose )

Main Method.

Implements protocols::moves::Mover.

References copy_CCD_torsions().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general ( core::pose::Pose chain_break_screening_pose,
core::scoring::ScoreFunctionOP const &  chainbreak_scorefxn,
core::Size const  five_ 
bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::check_loop_closed ( core::pose::Pose const &  pose)
bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::check_screen ( )
bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::check_screen ( core::pose::Pose pose)
void protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::copy_CCD_torsions ( core::pose::Pose pose) const

References copy_CCD_torsions_general(), and five_prime_res_.

Referenced by apply().

void protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::copy_CCD_torsions_general ( core::pose::Pose pose,
core::Size const  five_prime_res,
core::Size const  three_prime_res 
) const
core::Size const& protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::five_prime_res ( ) const

References five_prime_res_.

std::string protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::get_name ( ) const

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

Implements protocols::moves::Mover.

core::pose::Pose& protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::pose ( )
void protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::set_reinitialize_CCD_torsions ( bool const &  setting)

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_scorefxn_
core::pose::Pose protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_pose_
StepWiseRNA_CountStruct protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::count_data_
core::Size const protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::five_prime_res_
bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::reinitialize_CCD_torsions_
bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::verbose_

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