Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter Class Reference

#include <RNA_FragmentMonteCarloOutputter.hh>

Inheritance diagram for protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter:
Inheritance graph

Public Member Functions

 RNA_FragmentMonteCarloOutputter (core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options, core::pose::PoseCOP align_pose)
 ~RNA_FragmentMonteCarloOutputter () override
void apply (core::pose::Pose &pose) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void output_running_info (core::Size const &r, core::Size const &i, core::pose::Pose &pose, core::scoring::ScoreFunctionCOP working_denovo_scorefxn)
void finalize (core::scoring::ScoreFunctionCOP denovo_scorefxn)
numeric::MathNTensorOP< core::Size, 6 > jump_histogram () const
void set_jump_histogram (numeric::MathNTensorOP< core::Size, 6 > 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions

void initialize (core::pose::PoseCOP align_pose)
core::kinematics::RT get_output_jump_RT (core::pose::PoseCOP pose) const
void get_output_jump_stub_stub (core::pose::Pose const &pose, core::kinematics::Stub &stub1, core::kinematics::Stub &stub2) const
void output_jump_information (core::pose::Pose const &pose)

Private Attributes

core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options_
utility::io::ozstream running_score_output_
numeric::MathNTensorOP< core::Size, 6 > jump_histogram_
utility::vector1< core::Realjump_histogram_min_
utility::vector1< core::Realjump_histogram_max_
utility::vector1< core::Realjump_histogram_bin_width_
core::pose::rna::StubStubType output_stub_stub_type_
core::kinematics::RTOP reference_RT_

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

◆ RNA_FragmentMonteCarloOutputter()

protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::RNA_FragmentMonteCarloOutputter ( core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP  options,
core::pose::PoseCOP  align_pose 

References initialize().

◆ ~RNA_FragmentMonteCarloOutputter()

protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::~RNA_FragmentMonteCarloOutputter ( )

Member Function Documentation

◆ apply()

void protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::apply ( core::pose::Pose )

Main Method.

Implements protocols::moves::Mover.

◆ finalize()

void protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::finalize ( core::scoring::ScoreFunctionCOP  denovo_scorefxn)

◆ get_name()

std::string protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ get_output_jump_RT()

core::kinematics::RT protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::get_output_jump_RT ( core::pose::PoseCOP  pose) const

◆ get_output_jump_stub_stub()

void protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::get_output_jump_stub_stub ( core::pose::Pose const &  pose,
core::kinematics::Stub stub1,
core::kinematics::Stub stub2 
) const

◆ initialize()

void protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::initialize ( core::pose::PoseCOP  align_pose)

◆ jump_histogram()

numeric::MathNTensorOP< core::Size, 6 > protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::jump_histogram ( ) const

References jump_histogram_.

◆ output_jump_information()

void protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::output_jump_information ( core::pose::Pose const &  pose)

◆ output_running_info()

void protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::output_running_info ( core::Size const &  r,
core::Size const &  i,
core::pose::Pose pose,
core::scoring::ScoreFunctionCOP  working_denovo_scorefxn 

◆ set_jump_histogram()

void protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::set_jump_histogram ( numeric::MathNTensorOP< core::Size, 6 >  setting)

References jump_histogram_.

Member Data Documentation

◆ jump_histogram_

numeric::MathNTensorOP< core::Size, 6 > protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::jump_histogram_

◆ jump_histogram_bin_width_

utility::vector1< core::Real > protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::jump_histogram_bin_width_

◆ jump_histogram_max_

utility::vector1< core::Real > protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::jump_histogram_max_

Referenced by finalize(), and initialize().

◆ jump_histogram_min_

utility::vector1< core::Real > protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::jump_histogram_min_

◆ options_

core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::options_

◆ output_stub_stub_type_

core::pose::rna::StubStubType protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::output_stub_stub_type_

◆ reference_RT_

core::kinematics::RTOP protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::reference_RT_

◆ running_score_output_

utility::io::ozstream protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::running_score_output_

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