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Public Member Functions | Private Attributes | List of all members
protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler Class Reference

#include <RNA_ChiStepWiseSampler.hh>

Inheritance diagram for protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler:
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Public Member Functions

 RNA_ChiStepWiseSampler (core::Size const rsd_id, core::chemical::rna::PuckerState const pucker_state, core::chemical::rna::ChiState const base_state)
 
void init () override
 Initialization. More...
 
void set_rsd_id (core::Size const setting) override
 Set the residue id. More...
 
core::chemical::rna::PuckerState pucker_state ()
 Get the pucker state (NORTH / SOUTH) More...
 
void set_pucker_state (core::chemical::rna::PuckerState const setting)
 Set the pucker state (NORTH / SOUTH) More...
 
core::chemical::rna::ChiState base_state ()
 Get the base state (WHATEVER / ANTI / SYN) More...
 
void set_base_state (core::chemical::rna::ChiState const setting)
 Set the base state (WHATEVER / ANTI / SYN) More...
 
void set_bin_size (core::Real const setting)
 Set the bin_size (default: 20) More...
 
void set_max_range (core::Real const setting)
 Set the max_range of modeler (default: +-20) More...
 
void set_extra_chi (bool const setting)
 Set use extra chi (+-60) More...
 
void set_sample_all_chi (bool const &setting)
 
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::stepwise::sampler::StepWiseSamplerOneTorsion
 StepWiseSamplerOneTorsion ()
 
 StepWiseSamplerOneTorsion (core::id::TorsionID const &tor_id, TorsionList const &torsions)
 
 ~StepWiseSamplerOneTorsion () override
 
void apply (core::pose::Pose &pose) override
 Apply the current rotamer to pose. More...
 
void apply (core::pose::Pose &pose, core::Size const i) override
 Apply the i-th rotamer to pose. More...
 
virtual void set_torsions (TorsionList const &setting)
 Set the allowed torsions in sampler. More...
 
virtual void set_torsion_id (core::id::TorsionID const &setting)
 Set the TorsionID of the sampler. More...
 
std::string get_name () const override
 Name of the class. More...
 
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in SamplerPlusPlusTypes.hh) More...
 
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerOneValue
 StepWiseSamplerOneValue ()
 
 StepWiseSamplerOneValue (ValueList const &values)
 
 StepWiseSamplerOneValue (ValueList const &allowed_values, std::string const &name)
 
 ~StepWiseSamplerOneValue () override
 
void init () override
 Initialization. More...
 
void apply (core::pose::Pose &) override
 Apply the current rotamer to pose. More...
 
void apply (core::pose::Pose &, core::Size const) override
 Apply the i-th rotamer to pose. More...
 
core::Size size () const override
 Get the total number of rotamers in sampler. More...
 
virtual core::Real value () const
 Get the value of current value. More...
 
virtual core::Real value (core::Size const i) const
 Get the value of i-th value. More...
 
virtual void set_values (ValueList const &setting)
 Set the allowed values in sampler. More...
 
std::string get_name () const override
 Name of the class. More...
 
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in SamplerPlusPlusTypes.hh) More...
 
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSized
 StepWiseSamplerSized ()
 
 ~StepWiseSamplerSized () override
 
void init () override
 Initialization. More...
 
void reset () override
 Reset to the first (or random if 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...
 
std::string get_name () const override
 Name of the class. More...
 
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in SamplerPlusPlusTypes.hh) More...
 
core::Size const & id () const
 
virtual void fast_forward ()
 
virtual void set_id (core::Size const setting)
 
void show (std::ostream &out, core::Size const indent=0) const override
 output summary of class More...
 
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSampler
 StepWiseSampler ()
 
 ~StepWiseSampler () override
 
virtual bool random () const
 Check if is random modeler. More...
 
virtual void set_random (bool const setting)
 Set the random modeler state. 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 rsd_id_
 
core::chemical::rna::ChiState base_state_
 
core::chemical::rna::PuckerState pucker_state_
 
core::Real bin_size_
 
core::Real max_range_
 
bool sample_all_chi_
 
core::chemical::rna::RNA_FittedTorsionInfo const torsion_info_
 

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::stepwise::sampler::StepWiseSamplerOneValue
ValueList values_
 
- Protected Attributes inherited from protocols::stepwise::sampler::StepWiseSamplerSized
core::Size id_
 

Constructor & Destructor Documentation

◆ RNA_ChiStepWiseSampler()

protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::RNA_ChiStepWiseSampler ( core::Size const  rsd_id,
core::chemical::rna::PuckerState const  pucker_state,
core::chemical::rna::ChiState const  base_state 
)

Member Function Documentation

◆ base_state()

core::chemical::rna::ChiState protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::base_state ( )
inline

Get the base state (WHATEVER / ANTI / SYN)

References base_state_.

Referenced by RNA_ChiStepWiseSampler().

◆ get_name()

std::string protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::get_name ( ) const
inlineoverridevirtual

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

◆ init()

void protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::init ( void  )
overridevirtual

◆ pucker_state()

core::chemical::rna::PuckerState protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::pucker_state ( )
inline

Get the pucker state (NORTH / SOUTH)

References pucker_state_.

Referenced by RNA_ChiStepWiseSampler().

◆ set_base_state()

void protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_base_state ( core::chemical::rna::ChiState const  setting)
inline

Set the base state (WHATEVER / ANTI / SYN)

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

◆ set_bin_size()

void protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_bin_size ( core::Real const  setting)
inline

Set the bin_size (default: 20)

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

◆ set_extra_chi()

void protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_extra_chi ( bool const  setting)
inline

Set use extra chi (+-60)

References set_max_range().

◆ set_max_range()

void protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_max_range ( core::Real const  setting)
inline

Set the max_range of modeler (default: +-20)

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

Referenced by set_extra_chi().

◆ set_pucker_state()

void protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_pucker_state ( core::chemical::rna::PuckerState const  setting)
inline

Set the pucker state (NORTH / SOUTH)

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

◆ set_rsd_id()

void protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_rsd_id ( core::Size const  setting)
inlineoverridevirtual

◆ set_sample_all_chi()

void protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_sample_all_chi ( bool const &  setting)
inline

References max_range_, and sample_all_chi_.

◆ type()

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

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RNA_CHI.

Member Data Documentation

◆ base_state_

core::chemical::rna::ChiState protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::base_state_
private

Referenced by base_state(), init(), and set_base_state().

◆ bin_size_

core::Real protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::bin_size_
private

Referenced by init(), and set_bin_size().

◆ max_range_

core::Real protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::max_range_
private

◆ pucker_state_

core::chemical::rna::PuckerState protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::pucker_state_
private

◆ rsd_id_

core::Size protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::rsd_id_
private

Referenced by init(), and set_rsd_id().

◆ sample_all_chi_

bool protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::sample_all_chi_
private

Referenced by init(), and set_sample_all_chi().

◆ torsion_info_

core::chemical::rna::RNA_FittedTorsionInfo const protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::torsion_info_
private

Referenced by init().


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