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

#include <RNA_SuiteStepWiseSampler.hh>

Public Types

typedef utility::vector1
< core::Real
- 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

Public Member Functions

 RNA_SuiteStepWiseSampler (core::Size const rsd_id, PuckerState const pucker_state_lower, PuckerState const pucker_state_upper, ChiState const base_state_lower, ChiState const base_state_upper)
void init ()
 Initialization wrapper. More...
void init_standard ()
 Initialization for standard modeler. More...
void init_fast ()
 Initialization for fast mode. More...
void set_sample_nucleoside_lower (bool const setting)
 Set functions. More...
void set_sample_nucleoside_upper (bool const setting)
void set_extra_epsilon (bool const setting)
void set_extra_beta (bool const setting)
void set_extra_chi (bool const setting)
void set_skip_same_pucker (bool const setting)
void set_idealize_coord (bool const setting)
void set_fast (bool const setting)
 Fast mode: just sample popular center torsions. More...
void set_bin_size (core::Real const setting)
std::string get_name () const
 Name of the class. More...
virtual StepWiseSamplerType type () const
 Type of class (see enum in StepWiseSamplerTypes.hh) More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSizedAny
 StepWiseSamplerSizedAny ()
virtual ~StepWiseSamplerSizedAny ()
virtual void reset ()
 Reset to the first (or random if random()) rotamer. More...
virtual void operator++ ()
 Move to next rotamer. More...
virtual void apply (core::pose::Pose &pose)
 Apply the current rotamer to pose. More...
virtual void apply (core::pose::Pose &pose, Size const i)
 Apply the i-th rotamer to pose. More...
virtual core::Size size () const
 Get the total number of rotamers in sampler. More...
virtual void add_external_loop_rotamer (StepWiseSamplerSizedOP const &rotamer)
 Add one more rotamer sampler to this sampler. More...
virtual void clear_rotamer ()
 Clear all rotamer samplers stored in this sampler. More...
virtual void show (std::ostream &out, Size const indent=0) const
 output summary of class More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSized
 StepWiseSamplerSized ()
virtual ~StepWiseSamplerSized ()
virtual bool not_end () const
 Check if reach the end of rotamer list. More...
Size const & id () const
virtual void fast_forward ()
virtual void set_id (Size const setting)
- 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 Member Functions

TorsionList fast_sample_torsions_from_info (utility::vector1< core::chemical::rna::GaussianParameter > const &params)

Private Attributes

core::Size const rsd_id_
ChiState base_state_lower_
ChiState base_state_upper_
bool sample_nucleoside_lower_
bool sample_nucleoside_upper_
bool extra_epsilon_
bool extra_beta_
bool extra_chi_
bool skip_same_pucker_
bool idealize_coord_
bool fast_
core::Real bin_size_
utility::vector1< PuckerStatepucker_states_lower_
utility::vector1< PuckerStatepucker_states_upper_

Additional Inherited Members

- 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_

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::RNA_SuiteStepWiseSampler ( core::Size const  rsd_id,
PuckerState const  pucker_state_lower,
PuckerState const  pucker_state_upper,
ChiState const  base_state_lower,
ChiState const  base_state_upper 

Member Function Documentation

RNA_SuiteStepWiseSampler::TorsionList protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::fast_sample_torsions_from_info ( utility::vector1< core::chemical::rna::GaussianParameter > const &  params)

References center, and width.

Referenced by init_fast().

std::string protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::get_name ( ) const

Name of the class.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSizedAny.

References rsd_id_, and utility::to_string().

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init ( void  )
void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_fast ( )
void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard ( )
void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_bin_size ( core::Real const  setting)
void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_beta ( bool const  setting)
void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_chi ( bool const  setting)
void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_epsilon ( bool const  setting)
void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_fast ( bool const  setting)

Fast mode: just sample popular center torsions.

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

Set functions.

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_sample_nucleoside_upper ( bool const  setting)
void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_skip_same_pucker ( bool const  setting)
virtual StepWiseSamplerType protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::type ( ) const

Type of class (see enum in StepWiseSamplerTypes.hh)

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSizedAny.

References protocols::stepwise::sampler::RNA_SUITE.

Member Data Documentation

ChiState protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::base_state_lower_

Referenced by init_fast(), and init_standard().

ChiState protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::base_state_upper_

Referenced by init_fast(), and init_standard().

core::Real protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::bin_size_

Referenced by init_standard().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::extra_beta_

Referenced by init_fast(), and init_standard().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::extra_chi_

Referenced by init_fast(), and init_standard().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::extra_epsilon_

Referenced by init_fast(), and init_standard().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::fast_

Referenced by init(), and init_fast().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::idealize_coord_

Referenced by init_fast(), and init_standard().

utility::vector1<PuckerState> protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::pucker_states_lower_
utility::vector1<PuckerState> protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::pucker_states_upper_
core::Size const protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::rsd_id_

Referenced by get_name(), init_fast(), and init_standard().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::sample_nucleoside_lower_

Referenced by init(), init_fast(), and init_standard().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::sample_nucleoside_upper_

Referenced by init(), init_fast(), and init_standard().

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::skip_same_pucker_

Referenced by init_fast(), and init_standard().

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