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protocols::stepwise::sampler::rna::RNA_KinematicCloser Class Reference

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

#include <RNA_KinematicCloser.hh>

Inheritance diagram for protocols::stepwise::sampler::rna::RNA_KinematicCloser:
Inheritance graph
[legend]

Public Member Functions

 RNA_KinematicCloser (core::pose::Pose const &init_pose, core::Size const moving_suite, core::Size const chainbreak_suite, bool const is_TNA_=false)
 
 ~RNA_KinematicCloser () override
 
std::string get_name () const override
 Class name. More...
 
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh) More...
 
void init () override
 Initialization. More...
 
void init (const Pose &pose_current, const Pose &pose_closed, bool use_pose_closed=true)
 
void apply (core::pose::Pose &pose, core::Size const id) override
 Apply the i-th rotamer to pose. More...
 
core::Size size () const override
 Get the total number of rotamers in sampler. More...
 
void set_verbose (bool const setting)
 Set verbose. More...
 
void set_calculate_jacobians (bool const &setting)
 
bool calculate_jacobians () const
 
core::Real get_jacobian (Pose &pose) const
 Calculate the jacobian. More...
 
utility::vector1< core::Realget_all_jacobians () const
 
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSized
 StepWiseSamplerSized ()
 
 ~StepWiseSamplerSized () 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...
 
bool not_end () const override
 Check if reach the end of rotamer list. More...
 
void apply (core::pose::Pose &pose) override
 Apply the current rotamer to pose. 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...
 
core::Size const & id () const
 
virtual void fast_forward ()
 
virtual void set_id (core::Size const setting)
 
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::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

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

Private Attributes

core::pose::Pose const & init_pose_
 
core::Size const moving_suite_
 
core::Size const chainbreak_suite_
 
bool verbose_ = false
 
core::Size nsol_ = 0
 
utility::vector1
< core::id::NamedAtomID
atom_ids_
 
utility::vector1
< core::id::NamedAtomID
pivot_ids_
 
utility::vector1< core::Realoffset_save_
 
utility::vector1< core::Realall_jacobians_
 
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::fixedsizearray1
< core::Real, 3 > > 
atoms_
 
utility::vector1< core::Realdt_ang_
 
utility::vector1< core::Realdb_len_
 
utility::vector1< core::Realdb_ang_
 
bool calculate_jacobians_ = false
 
bool is_TNA_ = false
 

Additional Inherited Members

- Public Types inherited from protocols::toolbox::SamplerPlusPlus
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 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_
 

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::stepwise::sampler::rna::RNA_KinematicCloser::RNA_KinematicCloser ( core::pose::Pose const &  init_pose,
core::Size const  moving_suite,
core::Size const  chainbreak_suite,
bool const  is_TNA_ = false 
)
protocols::stepwise::sampler::rna::RNA_KinematicCloser::~RNA_KinematicCloser ( )
overridedefault
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 
)
overridevirtual
bool protocols::stepwise::sampler::rna::RNA_KinematicCloser::calculate_jacobians ( ) const
inline

References calculate_jacobians_.

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets ( core::pose::Pose const &  pose)
private
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_offset ( core::id::DOF_ID const &  dof_id,
core::Real const  original_torsion_value,
core::pose::Pose const &  pose 
)
private
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::fill_chainTORS ( core::pose::Pose const &  pose)
private

References atom_ids_, atoms_, db_ang_, db_len_, dt_ang_, and core::pose::Pose::xyz().

Referenced by init().

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_all_jacobians ( ) const
inline

References all_jacobians_.

Real protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_jacobian ( Pose pose) const
std::string protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_name ( ) const
inlineoverridevirtual

Class name.

Implements protocols::toolbox::SamplerPlusPlus.

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::init ( void  )
overridevirtual

Initialization.

Implements protocols::toolbox::SamplerPlusPlus.

References init_pose_.

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::init ( const Pose pose_current,
const Pose pose_closed,
bool  use_pose_closed = true 
)
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::operator= ( const RNA_KinematicCloser )
private
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::output_chainTORS ( ) const
private
void protocols::stepwise::sampler::rna::RNA_KinematicCloser::set_calculate_jacobians ( bool const &  setting)
inline

References calculate_jacobians_.

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
inlineoverridevirtual

Get the total number of rotamers in sampler.

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

References nsol_.

toolbox::SamplerPlusPlusType protocols::stepwise::sampler::rna::RNA_KinematicCloser::type ( ) const
inlineoverridevirtual

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RNA_KINEMATIC_CLOSER.

Member Data Documentation

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

Referenced by get_all_jacobians(), and init().

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

Referenced by fill_chainTORS(), and init().

utility::vector1< utility::fixedsizearray1< core::Real, 3 > > 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().

bool protocols::stepwise::sampler::rna::RNA_KinematicCloser::calculate_jacobians_ = false
private
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::pose::Pose const& protocols::stepwise::sampler::rna::RNA_KinematicCloser::init_pose_
private

Referenced by init().

bool protocols::stepwise::sampler::rna::RNA_KinematicCloser::is_TNA_ = false
private
core::Size const protocols::stepwise::sampler::rna::RNA_KinematicCloser::moving_suite_
private
core::Size protocols::stepwise::sampler::rna::RNA_KinematicCloser::nsol_ = 0
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().

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

Referenced by get_jacobian(), and init().

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_ = false
private

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