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protocols::swa::rna::RNA_LoopCloseSampler Class Reference

#include <RNA_LoopCloseSampler.hh>

Inheritance diagram for protocols::swa::rna::RNA_LoopCloseSampler:
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Collaboration diagram for protocols::swa::rna::RNA_LoopCloseSampler:
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Public Member Functions

 RNA_LoopCloseSampler (Size const moving_suite, Size const chainbreak_suite)
 
 ~RNA_LoopCloseSampler ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
utility::vector1
< utility::vector1< Real > > 
all_torsion_info ()
 
Size n_construct ()
 
void fill_pose (pose::Pose &pose, Size construct_number)
 
void clear_all ()
 
void set_bin_size (Size const setting)
 
void set_epsilon_range (Real const setting)
 
void set_rep_cutoff (Real const rep_cutoff)
 
void set_torsion_range (Real const torsion_range)
 
void set_torsion_increment (Real const torsion_increment)
 
void set_just_output_score (bool const setting)
 
void set_sample_only (bool const setting)
 
void set_sample_native_torsion (bool const setting)
 
void set_rbs_new_pair (utility::vector1< Real > const &rbs_new_pair)
 
void set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

bool torsion_angles_within_cutoffs (pose::Pose const &pose, Size const moving_suite, Size const chainbreak_suite)
 
void initialize_rep_scorefxn ()
 
Real initialize_fa_rep (pose::Pose const &pose, utility::vector1< Size > const &moving_suites, scoring::ScoreFunctionOP rep_scorefxn)
 
bool check_clash (pose::Pose &pose, Real const &fa_rep_score_baseline, Real const &rep_cutoff_, scoring::ScoreFunctionOP rep_scorefxn)
 

Private Attributes

Size const moving_suite_
 
Size const chainbreak_suite_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP rep_scorefxn_
 
Size bin_size_
 
Size n_construct_
 
Real rep_cutoff_
 
Real torsion_range_
 
Real torsion_increment_
 
Real epsilon_range_
 
bool just_output_score_
 
bool sample_only_
 
bool sample_native_torsion_
 
utility::vector1< Realrbs_new_pair_
 
utility::vector1< Realtorsion_info_
 
utility::vector1
< utility::vector1< Real > > 
all_torsion_info_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::swa::rna::RNA_LoopCloseSampler::RNA_LoopCloseSampler ( Size const  moving_suite,
Size const  chainbreak_suite 
)
protocols::swa::rna::RNA_LoopCloseSampler::~RNA_LoopCloseSampler ( )

Member Function Documentation

utility::vector1< utility::vector1< Real > > protocols::swa::rna::RNA_LoopCloseSampler::all_torsion_info ( )
inline
void protocols::swa::rna::RNA_LoopCloseSampler::apply ( core::pose::Pose pose_to_visualize)
virtual
bool protocols::swa::rna::RNA_LoopCloseSampler::check_clash ( pose::Pose pose,
Real const &  fa_rep_score_baseline,
Real const &  rep_cutoff_,
scoring::ScoreFunctionOP  rep_scorefxn 
)
private
void protocols::swa::rna::RNA_LoopCloseSampler::clear_all ( )
void protocols::swa::rna::RNA_LoopCloseSampler::fill_pose ( pose::Pose pose,
Size  construct_number 
)
virtual std::string protocols::swa::rna::RNA_LoopCloseSampler::get_name ( ) const
inlinevirtual

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

Implements protocols::moves::Mover.

Real protocols::swa::rna::RNA_LoopCloseSampler::initialize_fa_rep ( pose::Pose const &  pose,
utility::vector1< Size > const &  moving_suites,
scoring::ScoreFunctionOP  rep_scorefxn 
)
private
void protocols::swa::rna::RNA_LoopCloseSampler::initialize_rep_scorefxn ( )
private
Size protocols::swa::rna::RNA_LoopCloseSampler::n_construct ( )
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_bin_size ( Size const  setting)
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_epsilon_range ( Real const  setting)
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_just_output_score ( bool const  setting)
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_rbs_new_pair ( utility::vector1< Real > const &  rbs_new_pair)
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_rep_cutoff ( Real const  rep_cutoff)
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_sample_native_torsion ( bool const  setting)
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_sample_only ( bool const  setting)
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)
void protocols::swa::rna::RNA_LoopCloseSampler::set_torsion_increment ( Real const  torsion_increment)
inline
void protocols::swa::rna::RNA_LoopCloseSampler::set_torsion_range ( Real const  torsion_range)
inline
bool protocols::swa::rna::RNA_LoopCloseSampler::torsion_angles_within_cutoffs ( pose::Pose const &  pose,
Size const  moving_suite,
Size const  chainbreak_suite 
)
private

Member Data Documentation

utility::vector1< utility::vector1< Real > > protocols::swa::rna::RNA_LoopCloseSampler::all_torsion_info_
private

Referenced by apply(), clear_all(), and fill_pose().

Size protocols::swa::rna::RNA_LoopCloseSampler::bin_size_
private

Referenced by apply().

Size const protocols::swa::rna::RNA_LoopCloseSampler::chainbreak_suite_
private

Referenced by apply(), and fill_pose().

Real protocols::swa::rna::RNA_LoopCloseSampler::epsilon_range_
private

Referenced by apply().

bool protocols::swa::rna::RNA_LoopCloseSampler::just_output_score_
private
Size const protocols::swa::rna::RNA_LoopCloseSampler::moving_suite_
private

Referenced by apply(), and fill_pose().

Size protocols::swa::rna::RNA_LoopCloseSampler::n_construct_
private

Referenced by apply(), and clear_all().

utility::vector1< Real > protocols::swa::rna::RNA_LoopCloseSampler::rbs_new_pair_
private
Real protocols::swa::rna::RNA_LoopCloseSampler::rep_cutoff_
private

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::swa::rna::RNA_LoopCloseSampler::rep_scorefxn_
private

Referenced by apply(), and initialize_rep_scorefxn().

bool protocols::swa::rna::RNA_LoopCloseSampler::sample_native_torsion_
private

Referenced by apply().

bool protocols::swa::rna::RNA_LoopCloseSampler::sample_only_
private

Referenced by apply(), and initialize_fa_rep().

core::scoring::ScoreFunctionOP protocols::swa::rna::RNA_LoopCloseSampler::scorefxn_
private

Referenced by set_scorefxn().

Real protocols::swa::rna::RNA_LoopCloseSampler::torsion_increment_
private
utility::vector1< Real > protocols::swa::rna::RNA_LoopCloseSampler::torsion_info_
private

Referenced by apply().

Real protocols::swa::rna::RNA_LoopCloseSampler::torsion_range_
private

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