Public Member Functions | Private Member Functions | Private Attributes | List of all members
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

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::TorsionIDTorsionIDs

Additional Inherited Members

- Public Types inherited from protocols::toolbox::SamplerPlusPlus
typedef utility::vector1< core::RealTorsionList
- 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

◆ MC_RNA_KIC_Sampler() [1/2]

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 

◆ ~MC_RNA_KIC_Sampler()

protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::~MC_RNA_KIC_Sampler ( )

◆ MC_RNA_KIC_Sampler() [2/2]

protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::MC_RNA_KIC_Sampler ( const MC_RNA_KIC_Sampler )

Member Function Documentation

◆ apply()

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::apply ( core::pose::Pose pose)

◆ check_angles_in_range()

bool protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::check_angles_in_range ( const core::pose::Pose pose)

◆ check_moved()

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_.

◆ choose_solution()

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::choose_solution ( )

◆ find()

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

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_.

◆ get_jacobian()

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

References loop_closer_.

Referenced by apply().

◆ get_name()

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

Name of the class.

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

◆ get_next_solutions()

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

◆ init()

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::init ( void  )

◆ next()

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++().

◆ operator++()

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::operator++ ( )

◆ operator=()

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::operator= ( const MC_RNA_KIC_Sampler )

◆ reset()

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::reset ( void  )

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

Implements protocols::toolbox::SamplerPlusPlus.

◆ set_angle_range_from_init_torsions()

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

◆ set_gaussian_stdev()

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().

◆ set_max_tries()

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

Max # of step for trying in random samping.

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

◆ show()

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

◆ type()

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

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::MC_RNA_KIC.

◆ update()

void protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::update ( )

◆ vector_sum()

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

References sum_.

Member Data Documentation

◆ all_jacobians_

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

Referenced by choose_solution().

◆ angle_max_

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

◆ angle_min_

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

◆ bb_samplers_

utility::vector1<MC_OneTorsionOP> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::bb_samplers_

◆ chainbreak_suite_

core::Size const protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::chainbreak_suite_

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

◆ chi_rotamer_

MC_CombOP protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::chi_rotamer_

◆ chi_samplers_

utility::vector1<MC_OneTorsionOP> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::chi_samplers_

◆ copy_stored_jacobians_

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

◆ current_jacobians_

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

Referenced by apply(), and choose_solution().

◆ cutpoint_handler_

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

Referenced by apply(), and get_next_solutions().

◆ did_close_

bool protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::did_close_

◆ gaussian_stdev_

core::Real protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::gaussian_stdev_

Referenced by set_gaussian_stdev().

◆ initial_torsions_

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

◆ jacobian_sampler_

numeric::random::WeightedSampler protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::jacobian_sampler_

Referenced by choose_solution().

◆ loop_closer_

stepwise::sampler::rna::RNA_KinematicCloserOP protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::loop_closer_

◆ max_tries_

core::Size protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::max_tries_

◆ moving_suite_

core::Size const protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::moving_suite_

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

◆ solution_

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

Referenced by apply(), and choose_solution().

◆ stored_jacobians_

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

◆ stored_loop_closer_

stepwise::sampler::rna::RNA_KinematicCloserOP protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::stored_loop_closer_

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

◆ stored_pose_

core::pose::Pose protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::stored_pose_

◆ sugar_samplers_

utility::vector1<MC_RNA_SugarOP> protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::sugar_samplers_

◆ sum_

core::Real protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::sum_

Referenced by vector_sum().

◆ TorsionIDs

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

◆ used_current_solution_

bool protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::used_current_solution_

Referenced by apply(), and update().

◆ verbose_

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

Referenced by init().

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