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protocols::stepwise::sampler::rna::RNA_KIC_Sampler Class Reference

#include <RNA_KIC_Sampler.hh>

Inheritance diagram for protocols::stepwise::sampler::rna::RNA_KIC_Sampler:
Inheritance graph
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Public Member Functions

 RNA_KIC_Sampler (core::pose::PoseOP ref_pose, core::Size const moving_suite, core::Size const chainbreak_suite, bool const is_TNA=false)
 
 ~RNA_KIC_Sampler () override
 
void init () override
 Initialization. More...
 
void reset () override
 Reset to the first (or random if is_random()) rotamer. More...
 
void operator++ () override
 Move to next rotamer. More...
 
bool not_end () const override
 Check if reach the end of rotamer list. More...
 
void apply (core::pose::Pose &pose) override
 Apply the current rotamer to pose. More...
 
void apply ()
 Apply the current rotamer to ref_pose_. More...
 
void set_random (bool const setting) override
 Set the random modeler state. More...
 
bool closable () const
 If the chain is closable (random modeler only) More...
 
std::string get_name () const override
 Name of the class. More...
 
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh) More...
 
void set_verbose (bool const setting)
 
void set_extra_epsilon (bool const setting)
 
void set_extra_chi (bool const setting)
 
void set_sample_all_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 (core::chemical::rna::PuckerState const setting)
 
void set_base_state (core::chemical::rna::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 sampling. More...
 
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSampler
 StepWiseSampler ()
 
 ~StepWiseSampler () override
 
virtual bool random () const
 Check if is random modeler. More...
 
- Public Member Functions inherited from protocols::toolbox::SamplerPlusPlus
 SamplerPlusPlus ()
 
 ~SamplerPlusPlus () override
 
virtual void show (std::ostream &out, core::Size const indent) const
 output summary of class More...
 
- 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 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 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_
 
core::chemical::rna::PuckerState pucker_state_
 
core::chemical::rna::ChiState base_state_
 
core::Size sample_nucleoside_
 
core::Real bin_size_ = 20
 
core::Size max_tries_ = 100
 
bool verbose_ = false
 
bool extra_epsilon_ = false
 
bool extra_chi_ = false
 
bool sample_all_chi_ = false
 
bool skip_same_pucker_ = false
 
bool idealize_coord_ = false
 
bool torsion_screen_ = true
 
bool random_chain_closed_ = true
 
StepWiseSamplerSizedCombOP bb_rotamer_
 
RNA_KinematicCloserOP loop_closer_
 
RNA_ChiStepWiseSamplerOP chi_rotamer_
 
screener::RNA_TorsionScreenerOP screener_
 
bool is_TNA_ = false
 

Additional Inherited Members

- Public Types inherited from protocols::toolbox::SamplerPlusPlus
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 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::toolbox::SamplerPlusPlus
bool is_init () const
 return OP to the subsampler that controls exactly this torsion_id (assume only one). This is worked out in recces/sampler/MC_Sampler & derived classes – wouldn't be too hard to generalize to stepwise/sampler/ classes, too. 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  ref_pose,
core::Size const  moving_suite,
core::Size const  chainbreak_suite,
bool const  is_TNA = false 
)
protocols::stepwise::sampler::rna::RNA_KIC_Sampler::~RNA_KIC_Sampler ( )
overridedefault
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)
overridevirtual
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)

References random_chain_closed_.

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

Check if reach the end of rotamer list.

Reimplemented from protocols::stepwise::sampler::StepWiseSampler.

References bb_rotamer_, and protocols::toolbox::SamplerPlusPlus::is_init().

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

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator++ ( )
overridevirtual
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator= ( const RNA_KIC_Sampler )
private
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::reset ( void  )
overridevirtual
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_base_state ( core::chemical::rna::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 sampling.

References max_tries_, and protocols::toolbox::SamplerPlusPlus::set_and_reinit().

void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_pucker_state ( core::chemical::rna::PuckerState const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_random ( bool const  setting)
overridevirtual
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_all_chi ( bool const  setting)
inline
void protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_nucleoside ( core::Size const  setting)
inline

References sample_nucleoside_.

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
toolbox::SamplerPlusPlusType protocols::stepwise::sampler::rna::RNA_KIC_Sampler::type ( ) const
inlineoverridevirtual

Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RNA_KIC.

Member Data Documentation

core::chemical::rna::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_ = 20
private

Referenced by init(), set_bin_size(), and set_fast().

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_ = false
private

Referenced by init(), set_extra_chi(), and set_fast().

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

Referenced by init(), set_extra_epsilon(), and set_fast().

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

Referenced by init(), and set_idealize_coord().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::is_TNA_ = false
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_ = 100
private

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

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

Referenced by init(), and set_pucker_state().

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

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

core::pose::PoseOP const protocols::stepwise::sampler::rna::RNA_KIC_Sampler::ref_pose_
private
bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::sample_all_chi_ = false
private

Referenced by init(), set_fast(), and set_sample_all_chi().

core::Size protocols::stepwise::sampler::rna::RNA_KIC_Sampler::sample_nucleoside_
private

Referenced by init(), and set_sample_nucleoside().

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_ = false
private

Referenced by init(), and set_skip_same_pucker().

bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::torsion_screen_ = true
private
bool protocols::stepwise::sampler::rna::RNA_KIC_Sampler::verbose_ = false
private

Referenced by init(), and set_verbose().


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