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

#include <RNA_MC_Suite.hh>

Public Member Functions

 RNA_MC_Suite (core::Size const rsd_id)
void init ()
 Initialization. More...
void clear_rotamer ()
 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_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_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...
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::MC_Comb
 MC_Comb ()
virtual ~MC_Comb ()
virtual void reset ()
 Reset to the first (or random if random()) rotamer. More...
virtual void operator++ ()
 Move to next rotamer. More...
virtual void update ()
 Update the DOFs. More...
virtual void apply (core::pose::Pose &pose)
 Apply the current rotamer to pose. More...
virtual void set_uniform_modeler (bool const setting)
 Get uniform modeler state. More...
virtual void add_external_loop_rotamer (MC_StepWiseSamplerOP const &rotamer)
 Add one more rotamer sampler to this sampler. More...
- Public Member Functions inherited from protocols::stepwise::sampler::MC_StepWiseSampler
 MC_StepWiseSampler ()
virtual ~MC_StepWiseSampler ()
virtual bool uniform_modeler () const
 Get uniform modeler state. More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerBase
 StepWiseSamplerBase ()
virtual ~StepWiseSamplerBase ()
virtual bool not_end () const
 Check if there are more rotamers available. More...
virtual bool random () const
 Check if is random modeler. More...
virtual void set_random (bool const setting)
 Set the random modeler state. More...
virtual void show (std::ostream &out, Size const indent=0) const
 output summary of class 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

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 const a_form_range_
core::chemical::rna::PuckerState init_pucker_
utility::vector1< core::Reala_form_torsions_
utility::vector1< core::Realinit_torsions_
< core::id::TorsionID
utility::vector1< MC_OneTorsionOPbb_samplers_
utility::vector1< MC_OneTorsionOPchi_samplers_
utility::vector1< RNA_MC_SugarOPsugar_samplers_

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...

Constructor & Destructor Documentation

protocols::stepwise::sampler::rna::RNA_MC_Suite::RNA_MC_Suite ( core::Size const  rsd_id)

Member Function Documentation

void protocols::stepwise::sampler::rna::RNA_MC_Suite::clear_rotamer ( )

Clear all rotamer samplers stored in this sampler.

Reimplemented from protocols::stepwise::sampler::MC_Comb.

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

Referenced by init().

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

Name of the class.

Reimplemented from protocols::stepwise::sampler::MC_Comb.

void protocols::stepwise::sampler::rna::RNA_MC_Suite::init ( void  )
void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_gaussian_stdev ( core::Real const  setting)

Set the standard deviation of Gaussian sampler.

References bb_samplers_, chi_samplers_, gaussian_stdev_, and protocols::stepwise::sampler::StepWiseSamplerBase::is_init().

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

Set if using RNA_IdealCoord to sample puckers.

References idealize_coord_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit().

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

Set starting torsions and pucker states.

References init_pucker_, init_torsions_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_init().

void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_pucker_flip_rate ( core::Real const  setting)
void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_sample_bb ( bool const  setting)
void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_sample_lower_nucleoside ( bool const  setting)
void protocols::stepwise::sampler::rna::RNA_MC_Suite::set_sample_near_a_form ( bool const  setting)

Set if only sample near A form rotamers.

References sample_near_a_form_, and protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit().

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

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

References protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit(), and skip_same_pucker_.

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

Type of class (see enum in StepWiseSamplerTypes.hh)

Implements protocols::stepwise::sampler::StepWiseSamplerBase.

References protocols::stepwise::sampler::RNA_MC_SUITE.

Member Data Documentation

core::Real const protocols::stepwise::sampler::rna::RNA_MC_Suite::a_form_range_

Referenced by init().

utility::vector1<core::Real> protocols::stepwise::sampler::rna::RNA_MC_Suite::a_form_torsions_

Referenced by init(), and RNA_MC_Suite().

utility::vector1<MC_OneTorsionOP> protocols::stepwise::sampler::rna::RNA_MC_Suite::bb_samplers_
utility::vector1<MC_OneTorsionOP> protocols::stepwise::sampler::rna::RNA_MC_Suite::chi_samplers_
core::Real protocols::stepwise::sampler::rna::RNA_MC_Suite::gaussian_stdev_

Referenced by init(), and set_gaussian_stdev().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::idealize_coord_

Referenced by init(), and set_idealize_coord().

core::chemical::rna::PuckerState protocols::stepwise::sampler::rna::RNA_MC_Suite::init_pucker_
utility::vector1<core::Real> protocols::stepwise::sampler::rna::RNA_MC_Suite::init_torsions_
core::Real protocols::stepwise::sampler::rna::RNA_MC_Suite::pucker_flip_rate_

Referenced by init(), and set_pucker_flip_rate().

core::Size const protocols::stepwise::sampler::rna::RNA_MC_Suite::rsd_id_

Referenced by init(), and set_init_from_pose().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::sample_bb_

Referenced by init(), and set_sample_bb().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::sample_lower_nucleoside_
bool protocols::stepwise::sampler::rna::RNA_MC_Suite::sample_near_a_form_

Referenced by init(), and set_sample_near_a_form().

bool protocols::stepwise::sampler::rna::RNA_MC_Suite::sample_upper_nucleoside_
bool protocols::stepwise::sampler::rna::RNA_MC_Suite::skip_same_pucker_

Referenced by init(), and set_skip_same_pucker().

utility::vector1<RNA_MC_SugarOP> protocols::stepwise::sampler::rna::RNA_MC_Suite::sugar_samplers_
utility::vector1<core::id::TorsionID> protocols::stepwise::sampler::rna::RNA_MC_Suite::torsion_ids_

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