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protocols::rna::denovo::movers::RNA_Minimizer Class Reference

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

#include <RNA_Minimizer.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNA_Minimizer:
Inheritance graph
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Public Member Functions

 RNA_Minimizer (core::import_pose::options::RNA_MinimizerOptionsCOP options=nullptr)
 Construct the protocol object given the RNA fragment library to use. More...
 
protocols::moves::MoverOP clone () const override
 Clone this object. More...
 
void apply (core::pose::Pose &pose) override
 Apply the loop-rebuild protocol to the input pose. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
void set_perform_minimizer_run (bool const setting)
 
void set_options (core::import_pose::options::RNA_MinimizerOptionsCOP setting)
 
void set_include_default_linear_chainbreak (bool const setting)
 
void set_atom_level_domain_map (core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map)
 
void set_score_function (core::scoring::ScoreFunctionCOP scorefxn)
 
core::scoring::ScoreFunctionOP
const & 
score_function () const
 
core::scoring::ScoreFunctionOP clone_scorefxn () const
 
void set_skip_chi_min (bool const &setting)
 
bool skip_chi_min () const
 
void set_min_tol (float const &setting)
 
- 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 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

void o2prime_trials (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP const &scorefxn) const
 
void packing_trials (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn) const
 
void packing_trials (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn, utility::vector1< core::Size > residues_to_pack) const
 
void setup_movemap (core::kinematics::MoveMap &mm, core::pose::Pose &pose)
 
void update_atom_level_domain_map_with_extra_minimize_res (core::pose::Pose const &pose)
 
void update_atom_level_domain_map_to_move_rosetta_library_chunks ()
 

Private Attributes

core::import_pose::options::RNA_MinimizerOptionsCOP options_
 
core::Real const coord_sdev_
 
core::Real const coord_cst_weight_
 
bool perform_minimizer_run_
 
bool include_default_linear_chainbreak_
 
bool close_loops_
 
core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map_input_
 
core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map_
 
core::scoring::ScoreFunctionOP scorefxn_
 
bool skip_chi_min_
 
float min_tol_
 

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::rna::denovo::movers::RNA_Minimizer::RNA_Minimizer ( core::import_pose::options::RNA_MinimizerOptionsCOP  options = nullptr)

Construct the protocol object given the RNA fragment library to use.

Member Function Documentation

void protocols::rna::denovo::movers::RNA_Minimizer::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::rna::denovo::movers::RNA_Minimizer::clone ( ) const
inlineoverridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_Minimizer::clone_scorefxn ( ) const
inline

References scorefxn_.

std::string protocols::rna::denovo::movers::RNA_Minimizer::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::rna::denovo::movers::RNA_Minimizer::o2prime_trials ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP const &  scorefxn 
) const
private
void protocols::rna::denovo::movers::RNA_Minimizer::packing_trials ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP const &  packer_scorefxn 
) const
private

References core::pose::Pose::size().

Referenced by apply().

void protocols::rna::denovo::movers::RNA_Minimizer::packing_trials ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP const &  packer_scorefxn,
utility::vector1< core::Size residues_to_pack 
) const
private
core::scoring::ScoreFunctionOP const& protocols::rna::denovo::movers::RNA_Minimizer::score_function ( ) const
inline

References scorefxn_.

void protocols::rna::denovo::movers::RNA_Minimizer::set_atom_level_domain_map ( core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map)
inline
void protocols::rna::denovo::movers::RNA_Minimizer::set_include_default_linear_chainbreak ( bool const  setting)
inline
void protocols::rna::denovo::movers::RNA_Minimizer::set_min_tol ( float const &  setting)
inline

References min_tol_.

void protocols::rna::denovo::movers::RNA_Minimizer::set_options ( core::import_pose::options::RNA_MinimizerOptionsCOP  setting)
inline

References options_.

void protocols::rna::denovo::movers::RNA_Minimizer::set_perform_minimizer_run ( bool const  setting)
inline
void protocols::rna::denovo::movers::RNA_Minimizer::set_score_function ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

void protocols::rna::denovo::movers::RNA_Minimizer::set_skip_chi_min ( bool const &  setting)
inline

References skip_chi_min_.

void protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap ( core::kinematics::MoveMap mm,
core::pose::Pose pose 
)
private
void protocols::rna::denovo::movers::RNA_Minimizer::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References include_default_linear_chainbreak_, options_, perform_minimizer_run_, and scorefxn_.

Referenced by protocols::rna::denovo::movers::operator<<().

bool protocols::rna::denovo::movers::RNA_Minimizer::skip_chi_min ( ) const
inline

References skip_chi_min_.

void protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_to_move_rosetta_library_chunks ( )
private
void protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_with_extra_minimize_res ( core::pose::Pose const &  pose)
private

Member Data Documentation

core::pose::toolbox::AtomLevelDomainMapOP protocols::rna::denovo::movers::RNA_Minimizer::atom_level_domain_map_
private
core::pose::toolbox::AtomLevelDomainMapCOP protocols::rna::denovo::movers::RNA_Minimizer::atom_level_domain_map_input_
private

Referenced by apply(), and set_atom_level_domain_map().

bool protocols::rna::denovo::movers::RNA_Minimizer::close_loops_
private

Referenced by apply().

core::Real const protocols::rna::denovo::movers::RNA_Minimizer::coord_cst_weight_
private

Referenced by apply().

core::Real const protocols::rna::denovo::movers::RNA_Minimizer::coord_sdev_
private

Referenced by apply().

bool protocols::rna::denovo::movers::RNA_Minimizer::include_default_linear_chainbreak_
private
float protocols::rna::denovo::movers::RNA_Minimizer::min_tol_
private

Referenced by apply(), and set_min_tol().

core::import_pose::options::RNA_MinimizerOptionsCOP protocols::rna::denovo::movers::RNA_Minimizer::options_
private
bool protocols::rna::denovo::movers::RNA_Minimizer::perform_minimizer_run_
private
core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_Minimizer::scorefxn_
private
bool protocols::rna::denovo::movers::RNA_Minimizer::skip_chi_min_
private

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