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protocols::rna::setup::RNA_CSA_JobDistributor Class Reference

#include <RNA_CSA_JobDistributor.hh>

Inheritance diagram for protocols::rna::setup::RNA_CSA_JobDistributor:
Inheritance graph
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Public Member Functions

 RNA_CSA_JobDistributor (stepwise::monte_carlo::StepWiseMonteCarloOP stepwise_monte_carlo, std::string const &silent_file, core::Size const nstruct, core::Size const csa_bank_size, core::Real const csa_rmsd, bool const output_round_silent_files, bool const annealing)
 
 RNA_CSA_JobDistributor (protocols::rna::denovo::RNA_FragmentMonteCarloOP rna_fragment_monte_carlo, std::string const &silent_file, core::Size const nstruct, core::Size const csa_bank_size, core::Real const csa_rmsd, bool const output_round_silent_files, bool const annealing)
 
 ~RNA_CSA_JobDistributor () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void initialize (core::pose::Pose const &pose) override
 
bool has_another_job () override
 
- Public Member Functions inherited from protocols::rna::setup::RNA_JobDistributor
 RNA_JobDistributor (stepwise::monte_carlo::StepWiseMonteCarloOP stepwise_monte_carlo, std::string const &silent_file, core::Size const nstruct)
 
 RNA_JobDistributor (rna::denovo::RNA_FragmentMonteCarloOP rna_fragment_monte_carlo, std::string const &silent_file, core::Size const nstruct)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_superimpose_over_all (bool const &setting)
 
bool superimpose_over_all () const
 
- 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

core::Size get_updates (core::io::silent::SilentStructCOP s) const
 
void set_updates (core::io::silent::SilentStructOP s, core::Size const updates) const
 
void update_bank (core::pose::Pose &pose)
 
void read_in_silent_file ()
 
void write_out_silent_file (std::string const &silent_file="")
 
void write_out_round_silent_file ()
 
void put_lock_on_silent_file ()
 
void free_lock_on_silent_file ()
 
bool check_for_closeness (core::pose::Pose &pose_test, core::pose::Pose const &full_model_pose) const
 
core::Real average_pairwise_distance () const
 

Private Attributes

std::string const lock_file
 
core::Size const csa_bank_size_
 
core::Size const total_updates_
 
core::Real csa_rmsd_
 
bool const output_round_silent_files_
 
core::Size total_updates_so_far_
 
core::io::silent::SilentFileDataOP sfd_
 
bool const annealing_
 

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...
 
- Protected Attributes inherited from protocols::rna::setup::RNA_JobDistributor
stepwise::monte_carlo::StepWiseMonteCarloOP stepwise_monte_carlo_
 
rna::denovo::RNA_FragmentMonteCarloOP rna_fragment_monte_carlo_
 
std::string const silent_file_
 
core::Size const nstruct_
 
bool superimpose_over_all_
 
core::pose::PoseCOP start_pose_
 

Constructor & Destructor Documentation

protocols::rna::setup::RNA_CSA_JobDistributor::RNA_CSA_JobDistributor ( stepwise::monte_carlo::StepWiseMonteCarloOP  stepwise_monte_carlo,
std::string const &  silent_file,
core::Size const  nstruct,
core::Size const  csa_bank_size,
core::Real const  csa_rmsd,
bool const  output_round_silent_files,
bool const  annealing 
)
protocols::rna::setup::RNA_CSA_JobDistributor::RNA_CSA_JobDistributor ( protocols::rna::denovo::RNA_FragmentMonteCarloOP  rna_fragment_monte_carlo,
std::string const &  silent_file,
core::Size const  nstruct,
core::Size const  csa_bank_size,
core::Real const  csa_rmsd,
bool const  output_round_silent_files,
bool const  annealing 
)
protocols::rna::setup::RNA_CSA_JobDistributor::~RNA_CSA_JobDistributor ( )
overridedefault

Member Function Documentation

void protocols::rna::setup::RNA_CSA_JobDistributor::apply ( core::pose::Pose )
overridevirtual
Real protocols::rna::setup::RNA_CSA_JobDistributor::average_pairwise_distance ( ) const
private
bool protocols::rna::setup::RNA_CSA_JobDistributor::check_for_closeness ( core::pose::Pose pose_test,
core::pose::Pose const &  full_model_pose 
) const
private
void protocols::rna::setup::RNA_CSA_JobDistributor::free_lock_on_silent_file ( )
private

References lock_file.

Referenced by apply().

Size protocols::rna::setup::RNA_CSA_JobDistributor::get_updates ( core::io::silent::SilentStructCOP  s) const
private

Referenced by read_in_silent_file().

bool protocols::rna::setup::RNA_CSA_JobDistributor::has_another_job ( )
overridevirtual
void protocols::rna::setup::RNA_CSA_JobDistributor::initialize ( core::pose::Pose const &  pose)
overridevirtual
void protocols::rna::setup::RNA_CSA_JobDistributor::put_lock_on_silent_file ( )
private
void protocols::rna::setup::RNA_CSA_JobDistributor::read_in_silent_file ( )
private
void protocols::rna::setup::RNA_CSA_JobDistributor::set_updates ( core::io::silent::SilentStructOP  s,
core::Size const  updates 
) const
private

References core::id::to_string().

Referenced by update_bank().

void protocols::rna::setup::RNA_CSA_JobDistributor::update_bank ( core::pose::Pose pose)
private
void protocols::rna::setup::RNA_CSA_JobDistributor::write_out_round_silent_file ( )
private
void protocols::rna::setup::RNA_CSA_JobDistributor::write_out_silent_file ( std::string const &  silent_file = "")
private

Member Data Documentation

bool const protocols::rna::setup::RNA_CSA_JobDistributor::annealing_
private

Referenced by apply().

core::Size const protocols::rna::setup::RNA_CSA_JobDistributor::csa_bank_size_
private
core::Real protocols::rna::setup::RNA_CSA_JobDistributor::csa_rmsd_
private

Referenced by apply(), and check_for_closeness().

std::string const protocols::rna::setup::RNA_CSA_JobDistributor::lock_file
private
bool const protocols::rna::setup::RNA_CSA_JobDistributor::output_round_silent_files_
private

Referenced by apply().

core::io::silent::SilentFileDataOP protocols::rna::setup::RNA_CSA_JobDistributor::sfd_
private
core::Size const protocols::rna::setup::RNA_CSA_JobDistributor::total_updates_
private

Referenced by has_another_job().

core::Size protocols::rna::setup::RNA_CSA_JobDistributor::total_updates_so_far_
private

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