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protocols::recces::sampler::rna::MC_RNA_KIC_Sampler Class Reference

#include <MC_RNA_KIC_Sampler.hh>

Inheritance diagram for protocols::recces::sampler::rna::MC_RNA_KIC_Sampler:
Inheritance graph
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Public Member Functions

 MC_RNA_KIC_Sampler (core::pose::PoseCOP mc_pose, core::Size const moving_suite, core::Size const chainbreak_suite, bool const change_ft=true)
 
 ~MC_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...
 
void update () override
 Update rotamer. More...
 
void get_next_solutions (core::pose::Pose const &pose)
 
void choose_solution ()
 
void next (core::pose::Pose const &pose)
 
bool check_moved () const
 Did the pose move at all? More...
 
void apply (core::pose::Pose &pose) override
 Apply the current rotamer to pose. 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_gaussian_stdev (core::Real const setting)
 Set the standard deviation of Gaussian sampler. More...
 
void set_max_tries (core::Size const setting)
 Max # of step for trying in random samping. More...
 
void set_angle_range_from_init_torsions (core::Real const range)
 
void show (std::ostream &out, core::Size const indent=0) const override
 output summary of class More...
 
MC_SamplerOP find (core::id::TorsionID const &torsion_id) override
 return OP to the subsampler that controls exactly this torsion_id (assume only one). More...
 
- Public Member Functions inherited from protocols::recces::sampler::MC_Sampler
 MC_Sampler ()
 
 ~MC_Sampler () override
 
virtual void set_uniform_modeler (bool const setting)
 Set uniform modeler (instead of Gaussian) More...
 
virtual bool uniform_modeler () const
 Get uniform modeler state. More...
 
virtual void set_update_pose (core::pose::PoseCOP setting)
 set (optional) update_pose More...
 
bool found_move () const
 check if ++ did anything to pose. More...
 
void set_name (std::string const &setting)
 Set name of the class. More...
 
void restore (core::pose::Pose &)
 restore pose to state prior to this sampler's apply(). Would enable big speedup in monte carlo by obviating pose copies. More...
 
- Public Member Functions inherited from protocols::toolbox::SamplerPlusPlus
 SamplerPlusPlus ()
 
 ~SamplerPlusPlus () override
 
- 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

core::Real get_jacobian (core::pose::Pose &pose)
 
bool check_angles_in_range (const core::pose::Pose &pose)
 
 MC_RNA_KIC_Sampler (const MC_RNA_KIC_Sampler &)
 
void operator= (const MC_RNA_KIC_Sampler &)
 
core::Real vector_sum (utility::vector1< core::Real > const &vector)
 

Private Attributes

core::pose::Pose stored_pose_
 
core::Size const moving_suite_
 
core::Size const chainbreak_suite_
 
core::Real gaussian_stdev_
 
core::Real sum_
 
core::Size max_tries_
 
bool verbose_
 
bool did_close_
 
bool used_current_solution_
 
stepwise::sampler::rna::RNA_KinematicCloserOP loop_closer_
 
stepwise::sampler::rna::RNA_KinematicCloserOP stored_loop_closer_
 
stepwise::monte_carlo::mover::TransientCutpointHandlerOP cutpoint_handler_
 
utility::vector1< MC_OneTorsionOPbb_samplers_
 
utility::vector1< MC_OneTorsionOPchi_samplers_
 
MC_CombOP chi_rotamer_
 
utility::vector1< MC_RNA_SugarOPsugar_samplers_
 
utility::vector1< core::Realstored_jacobians_
 
utility::vector1< core::Realcurrent_jacobians_
 
core::Size solution_
 
numeric::random::WeightedSampler jacobian_sampler_
 
utility::vector1< core::Realall_jacobians_
 
utility::vector1< core::Realcopy_stored_jacobians_
 
utility::vector1< core::Realinitial_torsions_
 
utility::vector1< core::Realangle_min_
 
utility::vector1< core::Realangle_max_
 
utility::vector1
< core::id::TorsionID
TorsionIDs
 

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...
 
- Protected Attributes inherited from protocols::recces::sampler::MC_Sampler
bool found_move_
 used to prevent simulated tempering from counting move if its filtered out. More...
 
PoseCOP update_pose_
 optional: pose accumulating changes in markov chain monte carlo, can use for updating sampler. More...
 
std::string name_
 

Constructor & Destructor Documentation

protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::MC_RNA_KIC_Sampler ( core::pose::PoseCOP  mc_pose,
core::Size const  moving_suite,
core::Size const  chainbreak_suite,
bool const  change_ft = true 
)
protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::~MC_RNA_KIC_Sampler ( )
inlineoverride
protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::MC_RNA_KIC_Sampler ( const MC_RNA_KIC_Sampler )
private

Member Function Documentation

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::apply ( core::pose::Pose pose)
overridevirtual
bool protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::check_angles_in_range ( const core::pose::Pose pose)
private
bool protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::check_moved ( ) const

Did the pose move at all?

References protocols::recces::sampler::MC_Sampler::found_move_.

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::choose_solution ( )
MC_SamplerOP protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::find ( core::id::TorsionID const &  torsion_id)
overridevirtual

return OP to the subsampler that controls exactly this torsion_id (assume only one).

Implements protocols::recces::sampler::MC_Sampler.

References chainbreak_suite_, core::pose::rna::get_suite_torsion_ids(), and moving_suite_.

Real protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::get_jacobian ( core::pose::Pose pose)
private

References loop_closer_.

Referenced by apply().

std::string protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::get_name ( ) const
inlineoverridevirtual

Name of the class.

Reimplemented from protocols::recces::sampler::MC_Sampler.

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::get_next_solutions ( core::pose::Pose const &  pose)
void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::init ( void  )
overridevirtual
void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::next ( core::pose::Pose const &  pose)

References choose_solution(), and get_next_solutions().

Referenced by operator++().

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::operator++ ( )
overridevirtual
void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::operator= ( const MC_RNA_KIC_Sampler )
private
void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::reset ( void  )
inlineoverridevirtual

Reset to the first (or random if is_random()) rotamer.

Implements protocols::toolbox::SamplerPlusPlus.

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::set_angle_range_from_init_torsions ( core::Real const  range)
void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::set_gaussian_stdev ( core::Real const  setting)

Set the standard deviation of Gaussian sampler.

References bb_samplers_, gaussian_stdev_, and protocols::toolbox::SamplerPlusPlus::is_init().

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::set_max_tries ( core::Size const  setting)
inline

Max # of step for trying in random samping.

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

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::show ( std::ostream &  out,
core::Size const  indent = 0 
) const
overridevirtual

output summary of class

Reimplemented from protocols::toolbox::SamplerPlusPlus.

References chainbreak_suite_, moving_suite_, and core::id::to_string().

toolbox::SamplerPlusPlusType protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::type ( ) const
inlineoverridevirtual

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::MC_RNA_KIC.

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::update ( )
overridevirtual
Real protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::vector_sum ( utility::vector1< core::Real > const &  vector)
private

References sum_.

Member Data Documentation

utility::vector1<core::Real> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::all_jacobians_
private

Referenced by choose_solution().

utility::vector1<core::Real> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::angle_max_
private
utility::vector1<core::Real> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::angle_min_
private
utility::vector1<MC_OneTorsionOP> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::bb_samplers_
private
core::Size const protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::chainbreak_suite_
private

Referenced by find(), init(), and show().

MC_CombOP protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::chi_rotamer_
private
utility::vector1<MC_OneTorsionOP> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::chi_samplers_
private
utility::vector1<core::Real> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::copy_stored_jacobians_
private
utility::vector1< core::Real > protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::current_jacobians_
private

Referenced by apply(), and choose_solution().

stepwise::monte_carlo::mover::TransientCutpointHandlerOP protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::cutpoint_handler_
private

Referenced by apply(), and get_next_solutions().

bool protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::did_close_
private
core::Real protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::gaussian_stdev_
private

Referenced by set_gaussian_stdev().

utility::vector1<core::Real> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::initial_torsions_
private
numeric::random::WeightedSampler protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::jacobian_sampler_
private

Referenced by choose_solution().

stepwise::sampler::rna::RNA_KinematicCloserOP protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::loop_closer_
private
core::Size protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::max_tries_
private
core::Size const protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::moving_suite_
private

Referenced by find(), init(), and show().

core::Size protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::solution_
private

Referenced by apply(), and choose_solution().

utility::vector1< core::Real > protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::stored_jacobians_
private
stepwise::sampler::rna::RNA_KinematicCloserOP protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::stored_loop_closer_
private

Referenced by apply(), get_next_solutions(), and init().

core::pose::Pose protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::stored_pose_
private
utility::vector1<MC_RNA_SugarOP> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::sugar_samplers_
private
core::Real protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::sum_
private

Referenced by vector_sum().

utility::vector1< core::id::TorsionID > protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::TorsionIDs
private
bool protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::used_current_solution_
private

Referenced by apply(), and update().

bool protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::verbose_
private

Referenced by init().


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