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

The RNA de novo structure modeling protocol. More...

#include <RNA_KinematicCloser.hh>

Public Member Functions

 RNA_KinematicCloser (core::pose::PoseOP const &ref_pose, core::Size const moving_suite, core::Size const chainbreak_suite)
 
 ~RNA_KinematicCloser ()
 
std::string get_name () const
 Class name. More...
 
virtual StepWiseSamplerType type () const
 Type of class (see enum in StepWiseSamplerTypes.hh) More...
 
void init ()
 Initialization. More...
 
virtual void apply (core::pose::Pose &pose, core::Size const id)
 Apply the i-th rotamer to pose. More...
 
core::Size size () const
 Get the total number of rotamers in sampler. More...
 
void set_verbose (bool const setting)
 Set verbose. 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 Member Functions

void figure_out_dof_ids_and_offsets ()
 
void figure_out_offset (core::id::DOF_ID const &dof_id, core::Real const original_torsion_value)
 
void fill_chainTORS ()
 
void output_chainTORS () const
 
 RNA_KinematicCloser (const RNA_KinematicCloser &)
 
void operator= (const RNA_KinematicCloser &)
 

Private Attributes

core::pose::PoseOP ref_pose_
 
core::Size const moving_suite_
 
core::Size const chainbreak_suite_
 
bool verbose_
 
core::Size nsol_
 
utility::vector1
< core::id::NamedAtomID
atom_ids_
 
utility::vector1< core::Realoffset_save_
 
utility::vector1
< core::id::DOF_ID
dof_ids_
 
utility::vector1
< utility::vector1< core::Real > > 
t_ang_
 
utility::vector1
< utility::vector1< core::Real > > 
b_ang_
 
utility::vector1
< utility::vector1< core::Real > > 
b_len_
 
utility::vector1
< utility::vector1< core::Real > > 
atoms_
 
utility::vector1< core::Realdt_ang_
 
utility::vector1< core::Realdb_len_
 
utility::vector1< core::Realdb_ang_
 

Additional Inherited Members

- Public Types inherited from protocols::stepwise::sampler::StepWiseSamplerBase
typedef utility::vector1
< core::Real
TorsionList
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
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_
 

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::stepwise::sampler::rna::RNA_KinematicCloser::RNA_KinematicCloser ( core::pose::PoseOP const &  ref_pose,
core::Size const  moving_suite,
core::Size const  chainbreak_suite 
)
protocols::stepwise::sampler::rna::RNA_KinematicCloser::~RNA_KinematicCloser ( )
protocols::stepwise::sampler::rna::RNA_KinematicCloser::RNA_KinematicCloser ( const RNA_KinematicCloser )
private

Member Function Documentation

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::apply ( core::pose::Pose pose,
core::Size const  id 
)
virtual
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets ( )
private
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_offset ( core::id::DOF_ID const &  dof_id,
core::Real const  original_torsion_value 
)
private
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::fill_chainTORS ( )
private
std::string protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_name ( ) const
inlinevirtual

Class name.

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

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::init ( void  )
virtual
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::operator= ( const RNA_KinematicCloser )
private
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::output_chainTORS ( ) const
private

References db_ang_, db_len_, dt_ang_, F, I, and protocols::stepwise::sampler::rna::TR.

Referenced by init().

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::set_verbose ( bool const  setting)
inline

Set verbose.

References verbose_.

core::Size protocols::stepwise::sampler::rna::RNA_KinematicCloser::size ( ) const
inlinevirtual

Get the total number of rotamers in sampler.

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

References nsol_.

virtual StepWiseSamplerType protocols::stepwise::sampler::rna::RNA_KinematicCloser::type ( ) const
inlinevirtual

Type of class (see enum in StepWiseSamplerTypes.hh)

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

References protocols::stepwise::sampler::RNA_KINEMATIC_CLOSER.

Member Data Documentation

utility::vector1< core::id::NamedAtomID > protocols::stepwise::sampler::rna::RNA_KinematicCloser::atom_ids_
private

Referenced by fill_chainTORS(), and init().

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::sampler::rna::RNA_KinematicCloser::atoms_
private

Referenced by fill_chainTORS(), and init().

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::sampler::rna::RNA_KinematicCloser::b_ang_
private

Referenced by init().

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::sampler::rna::RNA_KinematicCloser::b_len_
private

Referenced by init().

core::Size const protocols::stepwise::sampler::rna::RNA_KinematicCloser::chainbreak_suite_
private
utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::db_ang_
private
utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::db_len_
private
utility::vector1< core::id::DOF_ID > protocols::stepwise::sampler::rna::RNA_KinematicCloser::dof_ids_
private

Referenced by apply(), figure_out_offset(), and init().

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::dt_ang_
private
core::Size const protocols::stepwise::sampler::rna::RNA_KinematicCloser::moving_suite_
private
core::Size protocols::stepwise::sampler::rna::RNA_KinematicCloser::nsol_
private

Referenced by apply(), init(), and size().

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::offset_save_
private

Referenced by apply(), figure_out_offset(), and init().

core::pose::PoseOP protocols::stepwise::sampler::rna::RNA_KinematicCloser::ref_pose_
private
utility::vector1< utility::vector1< core::Real > > protocols::stepwise::sampler::rna::RNA_KinematicCloser::t_ang_
private

Referenced by apply(), and init().

bool protocols::stepwise::sampler::rna::RNA_KinematicCloser::verbose_
private

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