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protocols::recces::sampler::MC_OneTorsion Class Reference

#include <MC_OneTorsion.hh>

Inheritance diagram for protocols::recces::sampler::MC_OneTorsion:
Inheritance graph

Public Member Functions

 MC_OneTorsion (core::id::TorsionID const &tor_id, core::Real const start_torsion)
void init () override
 Initialization. More...
void reset () override
 Reset to current angle. More...
void operator++ () override
 Update the active angle based on stored (do not update stored_angle_) More...
void update () override
 Update the stored angle to match active angle. More...
void apply (core::pose::Pose &pose) override
 Apply the active torsion to pose. More...
core::Real stored_angle () const
 Get the stored angle. More...
core::Real active_angle () const
 Get the active angle. More...
void set_angle (core::Real const setting)
 Set the stored angle. More...
void set_angle_range (core::Real const min, core::Real const max)
 Set the angle range. More...
void set_gaussian_stdev (core::Real const setting)
 Set the standard deviation of Gaussian sampler. More...
void set_update_tolerance (core::Real const &setting)
void set_torsion_id (core::id::TorsionID const &setting)
 Set the TorsionID of the sampler. More...
core::id::TorsionID const & get_torsion_id () const
 Get the TorsionID of the sampler. More...
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...
void show (std::ostream &out, core::Size const indent) const override
 output summary of class More...
MC_SamplerOP find (core::id::TorsionID const &torsion_id) override
 return OP to the subsampler that controls exactly this torsion_id (assume only one). More...
- Public Member Functions inherited from protocols::recces::sampler::MC_Sampler
 MC_Sampler ()
 ~MC_Sampler () override
virtual void set_uniform_modeler (bool const setting)
 Set uniform modeler (instead of Gaussian) More...
virtual bool uniform_modeler () const
 Get uniform modeler state. More...
virtual void set_update_pose (core::pose::PoseCOP setting)
 set (optional) update_pose More...
bool found_move () const
 check if ++ did anything to pose. More...
std::string get_name () const override
 Name of the class. More...
void set_name (std::string const &setting)
 Set name of the class. More...
void restore (core::pose::Pose &)
 restore pose to state prior to this sampler's apply(). Would enable big speedup in monte carlo by obviating pose copies. 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

bool check_angle_in_range (core::Real angle) const
void regularize_angle (core::Real &angle)

Private Attributes

core::Real stored_angle_
core::Real active_angle_
core::Real angle_min_
core::Real angle_max_
core::Real stdev_
core::id::TorsionID torsion_id_
core::Real update_tolerance_

Additional Inherited Members

- Public Types inherited from protocols::toolbox::SamplerPlusPlus
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::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::recces::sampler::MC_Sampler
bool found_move_
 used to prevent simulated tempering from counting move if its filtered out. More...
PoseCOP update_pose_
 optional: pose accumulating changes in markov chain monte carlo, can use for updating sampler. More...
std::string name_

Constructor & Destructor Documentation

protocols::recces::sampler::MC_OneTorsion::MC_OneTorsion ( core::id::TorsionID const &  tor_id,
core::Real const  start_torsion 

Member Function Documentation

core::Real protocols::recces::sampler::MC_OneTorsion::active_angle ( ) const

Get the active angle.

References active_angle_.

void protocols::recces::sampler::MC_OneTorsion::apply ( core::pose::Pose pose)

Apply the active torsion to pose.

Implements protocols::toolbox::SamplerPlusPlus.

References active_angle_, core::pose::Pose::set_torsion(), and torsion_id_.

bool protocols::recces::sampler::MC_OneTorsion::check_angle_in_range ( core::Real  angle) const

References angle_max_, and angle_min_.

Referenced by operator++().

MC_SamplerOP protocols::recces::sampler::MC_OneTorsion::find ( core::id::TorsionID const &  torsion_id)

return OP to the subsampler that controls exactly this torsion_id (assume only one).

Implements protocols::recces::sampler::MC_Sampler.

References torsion_id_.

std::string protocols::recces::sampler::MC_OneTorsion::get_name ( ) const

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

Referenced by show().

core::id::TorsionID const& protocols::recces::sampler::MC_OneTorsion::get_torsion_id ( ) const

Get the TorsionID of the sampler.

References torsion_id_.

void protocols::recces::sampler::MC_OneTorsion::init ( void  )
void protocols::recces::sampler::MC_OneTorsion::operator++ ( )
void protocols::recces::sampler::MC_OneTorsion::regularize_angle ( core::Real angle)

Referenced by operator++(), and update().

void protocols::recces::sampler::MC_OneTorsion::reset ( void  )

Reset to current angle.

Implements protocols::toolbox::SamplerPlusPlus.

References active_angle_, and stored_angle_.

Referenced by init().

void protocols::recces::sampler::MC_OneTorsion::set_angle ( core::Real const  setting)

Set the stored angle.

References stored_angle_.

Referenced by update().

void protocols::recces::sampler::MC_OneTorsion::set_angle_range ( core::Real const  min,
core::Real const  max 
void protocols::recces::sampler::MC_OneTorsion::set_gaussian_stdev ( core::Real const  setting)

Set the standard deviation of Gaussian sampler.

References protocols::recces::sampler::MC_Sampler::set_uniform_modeler(), and stdev_.

void protocols::recces::sampler::MC_OneTorsion::set_torsion_id ( core::id::TorsionID const &  setting)

Set the TorsionID of the sampler.

References torsion_id_.

void protocols::recces::sampler::MC_OneTorsion::set_update_tolerance ( core::Real const &  setting)

References update_tolerance_.

void protocols::recces::sampler::MC_OneTorsion::show ( std::ostream &  out,
core::Size const  indent 
) const

output summary of class

Reimplemented from protocols::toolbox::SamplerPlusPlus.

References angle_max_, angle_min_, get_name(), and torsion_id_.

core::Real protocols::recces::sampler::MC_OneTorsion::stored_angle ( ) const

Get the stored angle.

References stored_angle_.

toolbox::SamplerPlusPlusType protocols::recces::sampler::MC_OneTorsion::type ( ) const

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::MC_ONE_TORSION.

void protocols::recces::sampler::MC_OneTorsion::update ( )

Member Data Documentation

core::Real protocols::recces::sampler::MC_OneTorsion::active_angle_
core::Real protocols::recces::sampler::MC_OneTorsion::angle_max_
core::Real protocols::recces::sampler::MC_OneTorsion::angle_min_
core::Real protocols::recces::sampler::MC_OneTorsion::stdev_

Referenced by operator++(), and set_gaussian_stdev().

core::Real protocols::recces::sampler::MC_OneTorsion::stored_angle_
core::id::TorsionID protocols::recces::sampler::MC_OneTorsion::torsion_id_
core::Real protocols::recces::sampler::MC_OneTorsion::update_tolerance_

Referenced by set_update_tolerance(), and update().

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