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protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler Class Reference

#include <RNA_SugarStepWiseSampler.hh>

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

 RNA_SugarStepWiseSampler (core::Size const rsd_id, core::chemical::rna::PuckerState const pucker_state)
 
void init () override
 Initialization. More...
 
void apply (core::pose::Pose &pose, core::Size const i) override
 Apply the i-th rotamer to pose. More...
 
core::Size size () const override
 Get the total number of rotamers in sampler. More...
 
void set_rsd_id (core::Size const setting)
 Set the residue id being sampled. More...
 
core::Size const & rsd_id () const
 Get the residue id being sampled. More...
 
core::chemical::rna::PuckerState pucker () const
 Get the current pucker state. More...
 
void set_pucker_state (core::chemical::rna::PuckerState const setting)
 Set the pucker_state (WHATEVER / NORTH / SOUTH) 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...
 
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh) More...
 
std::string get_name () const override
 Name of the class. 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Attributes

utility::vector1
< core::chemical::rna::PuckerState
pucker_states_
 
core::Size rsd_id_
 
core::chemical::rna::PuckerState pucker_state_
 
bool skip_same_pucker_
 
bool idealize_coord_
 
std::map< core::id::DOF_ID,
core::Real
north_pucker_dof_key_values_
 
std::map< core::id::DOF_ID,
core::Real
south_pucker_dof_key_values_
 
bool north_pucker_dofs_have_not_been_initialized_
 
bool south_pucker_dofs_have_not_been_initialized_
 

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::stepwise::sampler::StepWiseSamplerSized
core::Size id_
 

Constructor & Destructor Documentation

protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::RNA_SugarStepWiseSampler ( core::Size const  rsd_id,
core::chemical::rna::PuckerState const  pucker_state 
)

Member Function Documentation

void protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::apply ( core::pose::Pose pose,
core::Size const  i 
)
overridevirtual
std::string protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::get_name ( ) const
overridevirtual

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

References rsd_id_, and core::id::to_string().

void protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::init ( void  )
overridevirtual
core::chemical::rna::PuckerState protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker ( ) const
inline
core::Size const& protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::rsd_id ( ) const
inline

Get the residue id being sampled.

References rsd_id_.

void protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_idealize_coord ( bool const  setting)
inline

Set if using RNA_IdealCoord to sample puckers.

References idealize_coord_.

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

Set the pucker_state (WHATEVER / NORTH / SOUTH)

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

void protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_rsd_id ( core::Size const  setting)
inline

Set the residue id being sampled.

References rsd_id_.

void protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_skip_same_pucker ( bool const  setting)
inline

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

References skip_same_pucker_.

core::Size protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::size ( ) const
inlineoverridevirtual

Get the total number of rotamers in sampler.

Implements protocols::stepwise::sampler::StepWiseSamplerSized.

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

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

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RNA_SUGAR.

Member Data Documentation

bool protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::idealize_coord_
private

Referenced by apply(), and set_idealize_coord().

std::map< core::id::DOF_ID , core::Real > protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::north_pucker_dof_key_values_
private

Referenced by apply().

bool protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::north_pucker_dofs_have_not_been_initialized_
private

Referenced by apply().

core::chemical::rna::PuckerState protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker_state_
private
utility::vector1<core::chemical::rna::PuckerState> protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker_states_
private

Referenced by apply(), init(), pucker(), and size().

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

Referenced by apply(), get_name(), rsd_id(), and set_rsd_id().

bool protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::skip_same_pucker_
private

Referenced by apply(), and set_skip_same_pucker().

std::map< core::id::DOF_ID , core::Real > protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::south_pucker_dof_key_values_
private

Referenced by apply().

bool protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::south_pucker_dofs_have_not_been_initialized_
private

Referenced by apply().


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