Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::sampler::rna::RNA_KIC_Sampler Class Reference

#include <RNA_KIC_Sampler.hh>

Public Member Functions

 RNA_KIC_Sampler (core::pose::PoseOP const &ref_pose, core::Size const moving_suite, core::Size const chainbreak_suite)
 
 ~RNA_KIC_Sampler ()
 
virtual void init ()
 Initialization. More...
 
virtual void reset ()
 Reset to the first (or random if is_random()) rotamer. More...
 
virtual void operator++ ()
 Move to next rotamer. More...
 
virtual bool not_end () const
 Check if reach the end of rotamer list. More...
 
void apply (core::pose::Pose &pose)
 Apply the current rotamer to pose. More...
 
void apply ()
 Apply the current rotamer to ref_pose_. More...
 
void set_random (bool const setting)
 Set the random modeler state. More...
 
bool closable () const
 If the chain is closable (random modeler only) More...
 
std::string get_name () const
 Name of the class. More...
 
virtual StepWiseSamplerType type () const
 Type of class (see enum in StepWiseSamplerTypes.hh) More...
 
void set_verbose (bool const setting)
 
void set_extra_epsilon (bool const setting)
 
void set_extra_chi (bool const setting)
 
void set_skip_same_pucker (bool const setting)
 
void set_idealize_coord (bool const setting)
 
void set_torsion_screen (bool const setting)
 
void set_pucker_state (PuckerState const setting)
 
void set_base_state (ChiState const setting)
 
void set_sample_nucleoside (core::Size const setting)
 
void set_bin_size (core::Real const setting)
 
void set_fast (core::Real const setting)
 
void set_max_tries (core::Size const setting)
 Max # of step for trying in random samping. More...
 
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerBase
 StepWiseSamplerBase ()
 
virtual ~StepWiseSamplerBase ()
 
virtual bool random () const
 Check if is random modeler. More...
 
virtual void show (std::ostream &out, Size const indent=0) const
 output summary of class More...
 
- 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
 
void set_type (std::string const &setting)
 
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
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

void get_next_valid_bb ()
 
 RNA_KIC_Sampler (const RNA_KIC_Sampler &)
 
void operator= (const RNA_KIC_Sampler &)
 

Private Attributes

core::pose::PoseOP const ref_pose_
 
core::Size const moving_suite_
 
core::Size const chainbreak_suite_
 
PuckerState pucker_state_
 
ChiState base_state_
 
core::Size sample_nucleoside_
 
core::Real bin_size_
 
core::Size max_tries_
 
bool verbose_
 
bool extra_epsilon_
 
bool extra_chi_
 
bool skip_same_pucker_
 
bool idealize_coord_
 
bool torsion_screen_
 
bool random_chain_closed_
 
StepWiseSamplerSizedCombOP bb_rotamer_
 
RNA_KinematicCloserOP loop_closer_
 
RNA_ChiStepWiseSamplerOP chi_rotamer_
 
screener::RNA_TorsionScreenerOP screener_
 

Additional Inherited Members

- Public Types inherited from protocols::stepwise::sampler::StepWiseSamplerBase
typedef utility::vector1
< core::Real
TorsionList
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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::stepwise::sampler::StepWiseSamplerBase
bool is_init () const
 Check if the sampler has been initialized. More...
 
void set_init (bool const setting)
 Set the initialization state. More...
 
template<class T >
void set_and_reinit (T &params, T const &setting)
 Set value of a parameter, return to pre-init state. 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::sampler::rna::RNA_KIC_Sampler::RNA_KIC_Sampler ( core::pose::PoseOP const &  ref_pose,
core::Size const  moving_suite,
core::Size const  chainbreak_suite 
)
protocols::stepwise::sampler::rna::RNA_KIC_Sampler::~RNA_KIC_Sampler ( )
protocols::stepwise::sampler::rna::RNA_KIC_Sampler::RNA_KIC_Sampler ( const RNA_KIC_Sampler )
private

Member Function Documentation

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply ( core::pose::Pose pose)
virtual
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply ( )

Apply the current rotamer to ref_pose_.

References ref_pose_.

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::closable ( ) const
inline

If the chain is closable (random modeler only)

std::string protocols::stepwise::sampler::rna::RNA_KIC_Sampler::get_name ( ) const
virtual
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::get_next_valid_bb ( )
private
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::init ( void  )
virtual
bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::not_end ( ) const
virtual

Check if reach the end of rotamer list.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerBase.

References bb_rotamer_, protocols::stepwise::sampler::StepWiseSamplerBase::is_init(), and runtime_assert.

Referenced by operator++(), and reset().

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator++ ( )
virtual
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator= ( const RNA_KIC_Sampler )
private
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::reset ( void  )
virtual
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_base_state ( ChiState const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_bin_size ( core::Real const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_extra_chi ( bool const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_extra_epsilon ( bool const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_fast ( core::Real const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_idealize_coord ( bool const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_max_tries ( core::Size const  setting)
inline

Max # of step for trying in random samping.

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_pucker_state ( PuckerState const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_random ( bool const  setting)
virtual
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_nucleoside ( core::Size const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_skip_same_pucker ( bool const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_torsion_screen ( bool const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_verbose ( bool const  setting)
inline
virtual StepWiseSamplerType protocols::stepwise::sampler::rna::RNA_KIC_Sampler::type ( ) const
inlinevirtual

Type of class (see enum in StepWiseSamplerTypes.hh)

Implements protocols::stepwise::sampler::StepWiseSamplerBase.

References protocols::stepwise::sampler::RNA_KIC.

Member Data Documentation

ChiState protocols::stepwise::sampler::rna::RNA_KIC_Sampler::base_state_
private
StepWiseSamplerSizedCombOP protocols::stepwise::sampler::rna::RNA_KIC_Sampler::bb_rotamer_
private
core::Real protocols::stepwise::sampler::rna::RNA_KIC_Sampler::bin_size_
private

Referenced by init().

core::Size const protocols::stepwise::sampler::rna::RNA_KIC_Sampler::chainbreak_suite_
private
RNA_ChiStepWiseSamplerOP protocols::stepwise::sampler::rna::RNA_KIC_Sampler::chi_rotamer_
private
bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::extra_chi_
private

Referenced by init().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::extra_epsilon_
private

Referenced by init().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::idealize_coord_
private

Referenced by init().

RNA_KinematicCloserOP protocols::stepwise::sampler::rna::RNA_KIC_Sampler::loop_closer_
private
core::Size protocols::stepwise::sampler::rna::RNA_KIC_Sampler::max_tries_
private

Referenced by operator++().

core::Size const protocols::stepwise::sampler::rna::RNA_KIC_Sampler::moving_suite_
private
PuckerState protocols::stepwise::sampler::rna::RNA_KIC_Sampler::pucker_state_
private

Referenced by init().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::random_chain_closed_
private

Referenced by apply(), and operator++().

core::pose::PoseOP const protocols::stepwise::sampler::rna::RNA_KIC_Sampler::ref_pose_
private
core::Size protocols::stepwise::sampler::rna::RNA_KIC_Sampler::sample_nucleoside_
private

Referenced by init().

screener::RNA_TorsionScreenerOP protocols::stepwise::sampler::rna::RNA_KIC_Sampler::screener_
private

Referenced by get_next_valid_bb(), and operator++().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::skip_same_pucker_
private

Referenced by init().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::torsion_screen_
private

Referenced by get_next_valid_bb(), and operator++().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::verbose_
private

Referenced by init().


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