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

#include <RNA_AddDeleteMonteCarlo.hh>

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 ()
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
virtual std::string get_name () const
 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 (Size const setting)
void set_output_period (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 ~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 initialize_next_suite_atoms ()
void output_silent_file (core::pose::Pose &pose, 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_
Size num_cycles_
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::SilentFileDataOP silent_file_data_
utility::vector1< std::stringnext_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::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::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 ( )

Member Function Documentation

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

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 ( )

References next_suite_atoms_.

Referenced by RNA_AddDeleteMonteCarlo().

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

References do_add_delete_.

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

References kT_.

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

References num_cycles_.

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

References output_period_.

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

References sample_range_large_.

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

References sample_range_small_.

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

References silent_file_.

Member Data Documentation

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

Referenced by apply(), and set_do_add_delete().

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

Referenced by apply(), and set_kT().

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

Referenced by apply(), and set_num_cycles().

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

Referenced by apply(), and set_output_period().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply().

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

Referenced by apply(), and set_sample_range_large().

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

Referenced by apply(), and set_sample_range_small().

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

Referenced by apply().

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

Referenced by output_silent_file().

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