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protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser Class Reference

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

#include <RNA_AnalyticLoopCloser.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser:
Inheritance graph
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Public Member Functions

 RNA_AnalyticLoopCloser (core::Size const moving_suite, core::Size const chainbreak_suite)
 Construct the protocol object. More...
 
protocols::moves::MoverOP clone () const override
 Clone this object. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void apply (core::pose::Pose &pose) override
 Apply the loop-rebuild protocol to the input pose. More...
 
void choose_best_solution_based_on_score_function (core::scoring::ScoreFunctionOP scorefxn)
 
void choose_least_perturb_solution ()
 
void get_all_solutions (core::pose::Pose &pose, utility::vector1< core::pose::PoseOP > &pose_list)
 
core::Size nsol ()
 
void fill_solution (core::pose::Pose &pose, core::Size const n) const
 
utility::vector1< core::Realget_torsions (core::Size const n)
 
utility::vector1
< utility::vector1< core::Real > > 
get_torsions_for_all_solutions ()
 
- 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 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Member Functions

bool close_at_cutpoint (core::pose::Pose &pose)
 
void figure_out_dof_ids_and_offsets (core::pose::Pose const &pose, utility::vector1< core::Real > const &dt_ang)
 
void figure_out_offset (core::pose::Pose const &pose, core::id::DOF_ID const &dof_id, core::Real const &original_torsion_value, utility::vector1< core::Real > &offset_save)
 
void apply_solutions (core::pose::Pose &pose)
 
void output_chainTORS (utility::vector1< core::Real > const &dt_ang, utility::vector1< core::Real > const &db_ang, utility::vector1< core::Real > const &db_len) const
 
void fill_chainTORS (core::pose::Pose const &pose, utility::vector1< core::id::NamedAtomID > const &atom_ids, utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &atoms, utility::vector1< core::Real > &dt_ang, utility::vector1< core::Real > &db_ang, utility::vector1< core::Real > &db_len) const
 

Private Attributes

core::Size const moving_suite_
 
core::Size const chainbreak_suite_
 
bool const verbose_
 
int nsol_
 
core::scoring::ScoreFunctionOP scorefxn_
 
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_
 
bool choose_least_perturb_solution_
 
bool choose_best_solution_
 

Additional Inherited Members

- 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::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...
 

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::RNA_AnalyticLoopCloser ( core::Size const  moving_suite,
core::Size const  chainbreak_suite 
)

Construct the protocol object.

Member Function Documentation

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::apply ( core::pose::Pose pose)
overridevirtual

Apply the loop-rebuild protocol to the input pose.

Apply the RNA Loop Closer – set up for Full Atom Representation.

Implements protocols::moves::Mover.

References close_at_cutpoint().

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::apply_solutions ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_best_solution_based_on_score_function ( core::scoring::ScoreFunctionOP  scorefxn)
void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_least_perturb_solution ( )
protocols::moves::MoverOP protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::clone ( ) const
overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

bool protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::close_at_cutpoint ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets ( core::pose::Pose const &  pose,
utility::vector1< core::Real > const &  dt_ang 
)
private
void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_offset ( core::pose::Pose const &  pose,
core::id::DOF_ID const &  dof_id,
core::Real const &  original_torsion_value,
utility::vector1< core::Real > &  offset_save 
)
private
void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::fill_chainTORS ( core::pose::Pose const &  pose,
utility::vector1< core::id::NamedAtomID > const &  atom_ids,
utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &  atoms,
utility::vector1< core::Real > &  dt_ang,
utility::vector1< core::Real > &  db_ang,
utility::vector1< core::Real > &  db_len 
) const
private
void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::fill_solution ( core::pose::Pose pose,
core::Size const  n 
) const
void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_all_solutions ( core::pose::Pose pose,
utility::vector1< core::pose::PoseOP > &  pose_list 
)
std::string protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_name ( ) const
inlineoverridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

utility::vector1< Real > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_torsions ( core::Size const  n)

References offset_save_, and t_ang_.

Referenced by get_torsions_for_all_solutions().

utility::vector1< utility::vector1< Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_torsions_for_all_solutions ( )

References get_torsions(), and t_ang_.

core::Size protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::nsol ( )
inline

References nsol_.

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::output_chainTORS ( utility::vector1< core::Real > const &  dt_ang,
utility::vector1< core::Real > const &  db_ang,
utility::vector1< core::Real > const &  db_len 
) const
private

Member Data Documentation

utility::vector1< core::id::NamedAtomID > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::atom_ids_
private
utility::vector1< utility::vector1< core::Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::b_ang_
private
utility::vector1< utility::vector1< core::Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::b_len_
private
core::Size const protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::chainbreak_suite_
private
bool protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_best_solution_
private
bool protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_least_perturb_solution_
private
utility::vector1< core::id::DOF_ID > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::dof_ids_
private
core::Size const protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::moving_suite_
private
int protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::nsol_
private
utility::vector1< core::Real > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::offset_save_
private
core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::scorefxn_
private
utility::vector1< utility::vector1< core::Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::t_ang_
private
bool const protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::verbose_
private

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