Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler Class Reference

#include <RNA_SugarStepWiseSampler.hh>

Public Member Functions

 RNA_SugarStepWiseSampler (core::Size const rsd_id, PuckerState const pucker_state)
void init ()
 Initialization. More...
void apply (core::pose::Pose &pose, core::Size const i)
 Apply the i-th rotamer to pose. More...
core::Size size () const
 Get the total number of rotamers in sampler. More...
void set_rsd_id (core::Size const setting)
 Set the residue id being sampled. More...
PuckerState pucker () const
 Get the current pucker state. More...
void set_pucker_state (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...
virtual StepWiseSamplerType type () const
 Type of class (see enum in StepWiseSamplerTypes.hh) More...
virtual std::string get_name () const
 Name of the class. More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSized
 StepWiseSamplerSized ()
virtual ~StepWiseSamplerSized ()
virtual void reset ()
 Reset to the first (or random if random()) rotamer. More...
virtual void operator++ ()
 Move to next rotamer. More...
virtual bool not_end () const
 Check if reach the end of rotamer list. More...
void apply (core::pose::Pose &pose)
 Apply the current rotamer to pose. More...
Size const & id () const
virtual void fast_forward ()
virtual void set_id (Size const setting)
virtual void show (std::ostream &out, Size const indent=0) const
 output summary of class More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerBase
 StepWiseSamplerBase ()
virtual ~StepWiseSamplerBase ()
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::moves::Mover
 Mover ()
virtual ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
void set_type (std::string const &setting)
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...
void set_current_tag (std::string const &new_tag)
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 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...
void type (const std::string &type_in)
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_type () const
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...
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 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...

Private Attributes

utility::vector1< PuckerStatepucker_states_
core::Size rsd_id_
PuckerState pucker_state_
bool skip_same_pucker_
bool idealize_coord_
std::map< core::id::DOF_ID,
std::map< core::id::DOF_ID,
bool north_pucker_dofs_have_not_been_initialized_
bool south_pucker_dofs_have_not_been_initialized_

Additional Inherited Members

- Public Types inherited from protocols::stepwise::sampler::StepWiseSamplerBase
typedef utility::vector1
< core::Real
- 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::stringStrings
- 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::stepwise::sampler::StepWiseSamplerBase
bool is_init () const
 Check if the sampler has been initialized. 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,
PuckerState const  pucker_state 

Member Function Documentation

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

Name of the class.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References rsd_id_, and utility::to_string().

void protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::init ( void  )
PuckerState protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker ( ) const

Get the current pucker state.

References runtime_assert.

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

Set if using RNA_IdealCoord to sample puckers.

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

Set the pucker_state (WHATEVER / NORTH / SOUTH)

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

Set the residue id being sampled.

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

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

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

Get the total number of rotamers in sampler.

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

References runtime_assert.

virtual StepWiseSamplerType protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::type ( ) const

Type of class (see enum in StepWiseSamplerTypes.hh)

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References protocols::stepwise::sampler::RNA_SUGAR.

Member Data Documentation

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

PuckerState protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker_state_

Referenced by init(), and RNA_SugarStepWiseSampler().

utility::vector1<PuckerState> protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker_states_

Referenced by apply(), and init().

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

Referenced by apply(), and get_name().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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