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protocols::recces::sampler::rna::MC_RNA_Suite Class Reference

#include <MC_RNA_Suite.hh>

Inheritance diagram for protocols::recces::sampler::rna::MC_RNA_Suite:
Inheritance graph
[legend]

Public Member Functions

 MC_RNA_Suite (core::Size const rsd_id)
 
void init () override
 Initialization. More...
 
void clear_rotamer () override
 Clear all rotamer samplers stored in this sampler. More...
 
void set_gaussian_stdev (core::Real const setting)
 Set the standard deviation of Gaussian sampler. More...
 
void set_angle_range_from_init (core::Real const setting)
 Set the angle range from the initial torsions. More...
 
void set_pucker_flip_rate (core::Real const setting)
 Set the flip rate of pucker. More...
 
void set_skip_same_pucker (bool const setting)
 Set if the sampler will skip pucker applying when input pose has. More...
 
void set_idealize_coord (bool const setting)
 Set if using RNA_IdealCoord to sample puckers. More...
 
void set_a_form_range (core::Real const setting)
 Set angle ranges for A form rotamers. More...
 
void set_sample_near_a_form (bool const setting)
 Set if only sample near A form rotamers. More...
 
void set_sample_bb (bool const setting)
 Set if sample backbone. More...
 
void set_sample_lower_nucleoside (bool const setting)
 Set if sample nucleoside. More...
 
void set_sample_upper_nucleoside (bool const setting)
 Set if sample nucleoside. More...
 
void set_init_states (utility::vector1< core::Real > const &init_torsions, core::chemical::rna::PuckerState const init_pucker)
 Set starting torsions and pucker states. More...
 
void set_init_from_pose (core::pose::Pose const &pose)
 Set starting torsions and pucker states from pose. More...
 
void set_angle (core::pose::Pose const &pose)
 Set the stored angle from a 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...
 
- Public Member Functions inherited from protocols::recces::sampler::MC_Comb
 MC_Comb ()
 
 ~MC_Comb () override
 
void reset () override
 Reset to the first (or random if random()) rotamer. More...
 
void operator++ () override
 Move to next rotamer. More...
 
void update () override
 Update the DOFs. More...
 
void apply (core::pose::Pose &pose) override
 Apply the current rotamer to pose. More...
 
void set_uniform_modeler (bool const setting) override
 Get uniform modeler state. More...
 
virtual void add_rotamer (MC_SamplerOP const &rotamer)
 Add one more rotamer sampler to this sampler. More...
 
void set_update_pose (core::pose::PoseCOP setting) override
 set (optional) update_pose More...
 
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...
 
core::Size num_rotamers () const
 
MC_SamplerOP operator[] (core::Size const id)
 
- Public Member Functions inherited from protocols::recces::sampler::MC_Sampler
 MC_Sampler ()
 
 ~MC_Sampler () override
 
virtual bool uniform_modeler () const
 Get uniform modeler state. 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 Attributes

core::Size const rsd_id_
 
bool skip_same_pucker_
 
bool idealize_coord_
 
bool sample_near_a_form_
 
bool sample_bb_
 
bool sample_lower_nucleoside_
 
bool sample_upper_nucleoside_
 
core::Real pucker_flip_rate_
 
core::Real gaussian_stdev_
 
core::Real angle_range_
 
core::Real a_form_range_
 
core::chemical::rna::PuckerState init_pucker_
 
utility::vector1< core::Reala_form_torsions_
 
utility::vector1< core::Realinit_torsions_
 
utility::vector1
< core::id::TorsionID
torsion_ids_
 
utility::vector1< MC_OneTorsionOPbb_samplers_
 
utility::vector1< MC_OneTorsionOPchi_samplers_
 
utility::vector1< MC_RNA_SugarOPsugar_samplers_
 

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_Comb
utility::vector1< MC_SamplerOProtamer_list_
 
- 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_Suite::MC_RNA_Suite ( core::Size const  rsd_id)

Member Function Documentation

void protocols::recces::sampler::rna::MC_RNA_Suite::clear_rotamer ( )
overridevirtual

Clear all rotamer samplers stored in this sampler.

Reimplemented from protocols::recces::sampler::MC_Comb.

References bb_samplers_, chi_samplers_, protocols::recces::sampler::MC_Comb::clear_rotamer(), and sugar_samplers_.

Referenced by init().

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

Name of the class.

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

void protocols::recces::sampler::rna::MC_RNA_Suite::init ( void  )
overridevirtual
void protocols::recces::sampler::rna::MC_RNA_Suite::set_a_form_range ( core::Real const  setting)
inline

Set angle ranges for A form rotamers.

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

void protocols::recces::sampler::rna::MC_RNA_Suite::set_angle ( core::pose::Pose const &  pose)

Set the stored angle from a pose.

References bb_samplers_, chi_samplers_, core::pose::Pose::torsion(), and torsion_ids_.

void protocols::recces::sampler::rna::MC_RNA_Suite::set_angle_range_from_init ( core::Real const  setting)

Set the angle range from the initial torsions.

References angle_range_, bb_samplers_, chi_samplers_, init_torsions_, and protocols::toolbox::SamplerPlusPlus::is_init().

void protocols::recces::sampler::rna::MC_RNA_Suite::set_gaussian_stdev ( core::Real const  setting)

Set the standard deviation of Gaussian sampler.

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

void protocols::recces::sampler::rna::MC_RNA_Suite::set_idealize_coord ( bool const  setting)
inline

Set if using RNA_IdealCoord to sample puckers.

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

void protocols::recces::sampler::rna::MC_RNA_Suite::set_init_from_pose ( core::pose::Pose const &  pose)
void protocols::recces::sampler::rna::MC_RNA_Suite::set_init_states ( utility::vector1< core::Real > const &  init_torsions,
core::chemical::rna::PuckerState const  init_pucker 
)
inline

Set starting torsions and pucker states.

References init_pucker_, init_torsions_, and protocols::toolbox::SamplerPlusPlus::set_init().

void protocols::recces::sampler::rna::MC_RNA_Suite::set_pucker_flip_rate ( core::Real const  setting)
void protocols::recces::sampler::rna::MC_RNA_Suite::set_sample_bb ( bool const  setting)
inline

Set if sample backbone.

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

void protocols::recces::sampler::rna::MC_RNA_Suite::set_sample_lower_nucleoside ( bool const  setting)
inline
void protocols::recces::sampler::rna::MC_RNA_Suite::set_sample_near_a_form ( bool const  setting)
inline

Set if only sample near A form rotamers.

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

void protocols::recces::sampler::rna::MC_RNA_Suite::set_sample_upper_nucleoside ( bool const  setting)
inline
void protocols::recces::sampler::rna::MC_RNA_Suite::set_skip_same_pucker ( bool const  setting)
inline

Set if the sampler will skip pucker applying when input pose has.

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

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

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

Reimplemented from protocols::recces::sampler::MC_Comb.

References protocols::toolbox::MC_RNA_SUITE.

Member Data Documentation

core::Real protocols::recces::sampler::rna::MC_RNA_Suite::a_form_range_
private

Referenced by init(), and set_a_form_range().

utility::vector1<core::Real> protocols::recces::sampler::rna::MC_RNA_Suite::a_form_torsions_
private

Referenced by init(), and MC_RNA_Suite().

core::Real protocols::recces::sampler::rna::MC_RNA_Suite::angle_range_
private

Referenced by init(), and set_angle_range_from_init().

utility::vector1<MC_OneTorsionOP> protocols::recces::sampler::rna::MC_RNA_Suite::bb_samplers_
private
utility::vector1<MC_OneTorsionOP> protocols::recces::sampler::rna::MC_RNA_Suite::chi_samplers_
private
core::Real protocols::recces::sampler::rna::MC_RNA_Suite::gaussian_stdev_
private

Referenced by init(), and set_gaussian_stdev().

bool protocols::recces::sampler::rna::MC_RNA_Suite::idealize_coord_
private

Referenced by init(), and set_idealize_coord().

core::chemical::rna::PuckerState protocols::recces::sampler::rna::MC_RNA_Suite::init_pucker_
private
utility::vector1<core::Real> protocols::recces::sampler::rna::MC_RNA_Suite::init_torsions_
private
core::Real protocols::recces::sampler::rna::MC_RNA_Suite::pucker_flip_rate_
private

Referenced by init(), and set_pucker_flip_rate().

core::Size const protocols::recces::sampler::rna::MC_RNA_Suite::rsd_id_
private

Referenced by init(), and set_init_from_pose().

bool protocols::recces::sampler::rna::MC_RNA_Suite::sample_bb_
private

Referenced by init(), and set_sample_bb().

bool protocols::recces::sampler::rna::MC_RNA_Suite::sample_lower_nucleoside_
private
bool protocols::recces::sampler::rna::MC_RNA_Suite::sample_near_a_form_
private

Referenced by init(), and set_sample_near_a_form().

bool protocols::recces::sampler::rna::MC_RNA_Suite::sample_upper_nucleoside_
private
bool protocols::recces::sampler::rna::MC_RNA_Suite::skip_same_pucker_
private

Referenced by init(), and set_skip_same_pucker().

utility::vector1<MC_RNA_SugarOP> protocols::recces::sampler::rna::MC_RNA_Suite::sugar_samplers_
private
utility::vector1<core::id::TorsionID> protocols::recces::sampler::rna::MC_RNA_Suite::torsion_ids_
private

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