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protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo Class Reference

#include <RNA_AddDeleteMonteCarlo.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo:
Inheritance graph
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Public Member Functions

 RNA_AddDeleteMonteCarlo (mover::AddOrDeleteMoverOP rna_add_or_delete_mover, RNA_TorsionMoverOP rna_torsion_mover, RNA_O2PrimeMoverOP rna_o2prime_mover, core::scoring::ScoreFunctionOP scorefxn)
 
 ~RNA_AddDeleteMonteCarlo () override
 
void apply (core::pose::Pose &pose_to_visualize) override
 Apply the minimizer to one pose. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_kT (core::Real const &setting)
 
void set_sample_range_small (core::Real const setting)
 
void set_sample_range_large (core::Real const setting)
 
void set_num_cycles (core::Size const setting)
 
void set_output_period (core::Size const setting)
 
void set_do_add_delete (bool const setting)
 
void set_silent_file (std::string 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 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 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 initialize_next_suite_atoms ()
 
void output_silent_file (core::pose::Pose &pose, core::Size const count)
 

Private Attributes

mover::AddOrDeleteMoverOP rna_add_or_delete_mover_
 
RNA_TorsionMoverOP rna_torsion_mover_
 
RNA_O2PrimeMoverOP rna_o2prime_mover_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Size num_cycles_
 
core::Size output_period_
 
core::Real sample_range_small_
 
core::Real sample_range_large_
 
core::Real kT_
 
bool do_add_delete_
 
std::string silent_file_
 
core::io::silent::SilentFileOptionsOP silent_file_options_
 
core::io::silent::SilentFileDataOP silent_file_data_
 
utility::vector1< std::string > next_suite_atoms_
 

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...
 

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::RNA_AddDeleteMonteCarlo ( mover::AddOrDeleteMoverOP  rna_add_or_delete_mover,
RNA_TorsionMoverOP  rna_torsion_mover,
RNA_O2PrimeMoverOP  rna_o2prime_mover,
core::scoring::ScoreFunctionOP  scorefxn 
)
protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::~RNA_AddDeleteMonteCarlo ( )
overridedefault

Member Function Documentation

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::apply ( core::pose::Pose pose_to_visualize)
overridevirtual
std::string protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::initialize_next_suite_atoms ( )
private

References next_suite_atoms_.

Referenced by RNA_AddDeleteMonteCarlo().

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file ( core::pose::Pose pose,
core::Size const  count 
)
private
void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::set_do_add_delete ( bool const  setting)
inline

References do_add_delete_.

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::set_kT ( core::Real const &  setting)
inline

References kT_.

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::set_num_cycles ( core::Size const  setting)
inline

References num_cycles_.

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::set_output_period ( core::Size const  setting)
inline

References output_period_.

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::set_sample_range_large ( core::Real const  setting)
inline

References sample_range_large_.

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::set_sample_range_small ( core::Real const  setting)
inline

References sample_range_small_.

void protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::set_silent_file ( std::string const &  setting)
inline

References silent_file_.

Member Data Documentation

bool protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::do_add_delete_
private

Referenced by apply(), and set_do_add_delete().

core::Real protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::kT_
private

Referenced by apply(), and set_kT().

utility::vector1< std::string > protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::next_suite_atoms_
private
core::Size protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::num_cycles_
private

Referenced by apply(), and set_num_cycles().

core::Size protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_period_
private

Referenced by apply(), and set_output_period().

mover::AddOrDeleteMoverOP protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::rna_add_or_delete_mover_
private

Referenced by apply().

RNA_O2PrimeMoverOP protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::rna_o2prime_mover_
private

Referenced by apply().

RNA_TorsionMoverOP protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::rna_torsion_mover_
private

Referenced by apply().

core::Real protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::sample_range_large_
private

Referenced by apply(), and set_sample_range_large().

core::Real protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::sample_range_small_
private

Referenced by apply(), and set_sample_range_small().

core::scoring::ScoreFunctionOP protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::scorefxn_
private

Referenced by apply().

std::string protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::silent_file_
private
core::io::silent::SilentFileDataOP protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::silent_file_data_
private

Referenced by output_silent_file().

core::io::silent::SilentFileOptionsOP protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::silent_file_options_
private

Referenced by output_silent_file().


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