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

#include <RNA_SuiteStepWiseSampler.hh>

Inheritance diagram for protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler:
Inheritance graph

Public Member Functions

 RNA_SuiteStepWiseSampler (core::Size const rsd_id, core::chemical::rna::PuckerState const pucker_state_lower, core::chemical::rna::PuckerState const pucker_state_upper, core::chemical::rna::ChiState const base_state_lower, core::chemical::rna::ChiState const base_state_upper, bool tna_lower=false, bool tna_upper=false)
void init () override
 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_sample_all_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 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::StepWiseSamplerSizedAny
 StepWiseSamplerSizedAny ()
 ~StepWiseSamplerSizedAny () 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...
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...
core::Size size () const override
 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...
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...
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::StepWiseSamplerSized
 StepWiseSamplerSized ()
 ~StepWiseSamplerSized () override
bool not_end () const override
 Check if reach the end of rotamer list. More...
core::Size const & id () const
virtual void fast_forward ()
virtual void set_id (core::Size const setting)
- 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 Member Functions

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

Private Attributes

core::Size const rsd_id_
core::chemical::rna::ChiState base_state_lower_
core::chemical::rna::ChiState base_state_upper_
bool tna_lower_ = false
bool tna_upper_ = false
bool sample_nucleoside_lower_ = true
bool sample_nucleoside_upper_ = true
bool extra_epsilon_ = false
bool extra_beta_ = false
bool extra_chi_ = false
bool sample_all_chi_ = false
bool skip_same_pucker_ = true
bool idealize_coord_ = true
bool fast_ = false
core::Real bin_size_ = 20
utility::vector1< core::chemical::rna::PuckerStatepucker_states_lower_
utility::vector1< core::chemical::rna::PuckerStatepucker_states_upper_

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::StepWiseSamplerSized
core::Size id_

Constructor & Destructor Documentation

◆ RNA_SuiteStepWiseSampler()

protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::RNA_SuiteStepWiseSampler ( core::Size const  rsd_id,
core::chemical::rna::PuckerState const  pucker_state_lower,
core::chemical::rna::PuckerState const  pucker_state_upper,
core::chemical::rna::ChiState const  base_state_lower,
core::chemical::rna::ChiState const  base_state_upper,
bool  tna_lower = false,
bool  tna_upper = false 

Member Function Documentation

◆ fast_sample_torsions_from_info()

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

◆ get_name()

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

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

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

◆ init()

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init ( void  )

◆ init_fast()

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_fast ( )

◆ init_standard()

void protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard ( )

◆ set_bin_size()

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

◆ set_extra_beta()

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

◆ set_extra_chi()

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

◆ set_extra_epsilon()

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

◆ set_fast()

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

Fast mode: just sample popular center torsions.

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

◆ set_idealize_coord()

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

◆ set_sample_all_chi()

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

◆ set_sample_nucleoside_lower()

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

◆ set_sample_nucleoside_upper()

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

◆ set_skip_same_pucker()

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

◆ type()

toolbox::SamplerPlusPlusType protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::type ( ) const

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RNA_SUITE.

Member Data Documentation

◆ base_state_lower_

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

Referenced by init_fast(), and init_standard().

◆ base_state_upper_

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

Referenced by init_fast(), and init_standard().

◆ bin_size_

core::Real protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::bin_size_ = 20

Referenced by init_standard(), and set_bin_size().

◆ extra_beta_

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

◆ extra_chi_

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

◆ extra_epsilon_

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

◆ fast_

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

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

◆ idealize_coord_

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

◆ pucker_states_lower_

utility::vector1<core::chemical::rna::PuckerState> protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::pucker_states_lower_

◆ pucker_states_upper_

utility::vector1<core::chemical::rna::PuckerState> protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::pucker_states_upper_

◆ rsd_id_

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

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

◆ sample_all_chi_

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::sample_all_chi_ = false

◆ sample_nucleoside_lower_

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

◆ sample_nucleoside_upper_

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

◆ skip_same_pucker_

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

◆ tna_lower_

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::tna_lower_ = false

Referenced by init_standard().

◆ tna_upper_

bool protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::tna_upper_ = false

Referenced by init_standard().

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