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protocols::jd2::RNA_DeNovoJobOutputter Class Reference

#include <RNA_DeNovoJobOutputter.hh>

Inheritance diagram for protocols::jd2::RNA_DeNovoJobOutputter:
Inheritance graph
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Public Types

typedef
protocols::jd2::FileJobOutputter 
parent
 
- Public Types inherited from protocols::jd2::FileJobOutputter
typedef
protocols::jd2::JobOutputter 
parent
 

Public Member Functions

 RNA_DeNovoJobOutputter ()
 
 ~RNA_DeNovoJobOutputter () override
 
void flush () override
 this function flushes any internal buffers - see parent class for explanation More...
 
void final_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag) override
 this function outputs the final result of a job. More...
 
void other_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false) override
 this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. —>these go to file silent_filename+tag More...
 
bool job_has_completed (JobCOP job) override
 this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to. This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever). This is the most basic form of checkpointing. More...
 
std::string output_name (JobCOP job) override
 this is the master function for determining the unique output identifier for a job More...
 
std::string filename (JobCOP) const override
 
void set_silent_file_name (utility::file::FileName const &name)
 
void set_forced_silent_struct_type (std::string const &)
 
void set_write_separate_scorefile (bool write_separate_scorefile)
 
void set_write_no_structures (bool value=true)
 
- Public Member Functions inherited from protocols::jd2::FileJobOutputter
 FileJobOutputter ()
 
 ~FileJobOutputter () override
 
void set_defaults ()
 
void file (JobCOP job, std::string const &data) override
 this function takes a string and writes it to disk (separately from Tracer output). More...
 
utility::file::FileName const & scorefile_name ()
 
bool write_scorefile () const
 
- Public Member Functions inherited from protocols::jd2::JobOutputter
 JobOutputter ()
 constructor – reads cmd-line to initialize evaluators More...
 
 ~JobOutputter () override
 
virtual void starting_pose (core::pose::Pose const &)
 optionally pass a starting (reference) pose to a JobOutputter for later comparison purposes and/or as interface for initializing evaluators More...
 
void add_evaluation (evaluation::PoseEvaluatorOP)
 
void set_evaluators (evaluation::PoseEvaluators const &)
 
void clear_evaluators ()
 clear the list of evaluators More...
 
evaluation::PoseEvaluatorsCOP evaluators () const
 
void evaluate (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const
 
void call_output_observers (core::pose::Pose const &pose, JobOP job) const
 call all output_observers More...
 
void set_defaults ()
 clear the list of evaluators More...
 

Protected Member Functions

core::io::silent::SilentStructOP dump_pose (utility::file::FileName const &filename, JobCOP job, core::pose::Pose const &pose, bool bWriteScoreOnly, int copy_count=-1, std::string const &suffix="")
 
- Protected Member Functions inherited from protocols::jd2::FileJobOutputter
virtual void scorefile (JobCOP job, core::pose::Pose const &pose, std::string prefix_tag="", std::string suffix_tag="", std::string scorefile="")
 this function will handle the scorefile. If you need to make it virtual do so. Latter two arguments are for redirecting the output to a different scorefile for "other_pose"s. Also adds StringReal job info to the score file. More...
 
- Protected Member Functions inherited from protocols::jd2::JobOutputter
std::string affixed_numbered_name (JobCOP job)
 this function generates the affixed, numbered name for the job as prefix + input + suffix + number (affixes from options system). This function is deliberately not virtual, this should be a common mechanism; your JobOutputter can not call it if it would like. More...
 

Private Member Functions

void add_silent_struct (core::io::silent::SilentStructOP ss, utility::file::FileName const &fn)
 
void set_defaults ()
 called by the constructor to set filename and options More...
 
void read_done_jobs ()
 
void write_all_structs ()
 this function is called at the end of job distribution to flush the buffers More...
 

Private Attributes

bool bWriteIntermediateFiles_
 
bool bWriteIntermediateStructures_
 
bool bWriteNoStructures_
 toggle to switch off writing of structures More...
 
bool write_separate_scorefile_
 whether to write a separate scorefile that contains the scorelines from the silent file More...
 
utility::file::FileName silent_file_
 
utility::vector1< std::string > silent_file_tags_
 
core::Size n_to_buffer_
 
core::Real random_flush_frequency_
 
utility::vector1< std::pair
< core::io::silent::SilentStructOP,
utility::file::FileName > > 
saved_structs_
 
std::string forced_silent_struct_type_
 override choice of silent_struct_type More...
 

Detailed Description

this is a implementation of JobOutputter for silent-file-based output.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::jd2::RNA_DeNovoJobOutputter::RNA_DeNovoJobOutputter ( )

References read_done_jobs(), and set_defaults().

protocols::jd2::RNA_DeNovoJobOutputter::~RNA_DeNovoJobOutputter ( )
override

Member Function Documentation

void protocols::jd2::RNA_DeNovoJobOutputter::add_silent_struct ( core::io::silent::SilentStructOP  ss,
utility::file::FileName const &  fn 
)
private

References saved_structs_.

Referenced by dump_pose().

core::io::silent::SilentStructOP protocols::jd2::RNA_DeNovoJobOutputter::dump_pose ( utility::file::FileName const &  filename,
JobCOP  job,
core::pose::Pose const &  pose,
bool  bWriteScoreOnly,
int  copy_count = -1,
std::string const &  suffix = "" 
)
protected
std::string protocols::jd2::RNA_DeNovoJobOutputter::filename ( JobCOP  ) const
inlineoverridevirtual

Reimplemented from protocols::jd2::JobOutputter.

References silent_file_.

Referenced by other_pose().

void protocols::jd2::RNA_DeNovoJobOutputter::final_pose ( JobOP  job,
core::pose::Pose const &  pose,
std::string const &  tag 
)
overridevirtual

this function outputs the final result of a job.

creating output functions/////////////////////////////////////////

Implements protocols::jd2::FileJobOutputter.

References bWriteNoStructures_, protocols::jd2::JobOutputter::call_output_observers(), dump_pose(), protocols::jd2::FileJobOutputter::scorefile(), silent_file_, and write_separate_scorefile_.

void protocols::jd2::RNA_DeNovoJobOutputter::flush ( )
overridevirtual

this function flushes any internal buffers - see parent class for explanation

Reimplemented from protocols::jd2::JobOutputter.

References write_all_structs().

bool protocols::jd2::RNA_DeNovoJobOutputter::job_has_completed ( JobCOP  job)
overridevirtual

this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to. This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever). This is the most basic form of checkpointing.

Implements protocols::jd2::FileJobOutputter.

References core::sequence::end, output_name(), core::scoring::pair, read_done_jobs(), saved_structs_, silent_file_tags_, and protocols::jd2::tr().

void protocols::jd2::RNA_DeNovoJobOutputter::other_pose ( JobOP  job,
core::pose::Pose const &  pose,
std::string const &  tag,
int  copy_count = -1,
bool  score_only = false 
)
overridevirtual

this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. —>these go to file silent_filename+tag

Implements protocols::jd2::FileJobOutputter.

References bWriteIntermediateFiles_, protocols::jd2::JobOutputter::call_output_observers(), dump_pose(), filename(), and silent_file_.

std::string protocols::jd2::RNA_DeNovoJobOutputter::output_name ( JobCOP  job)
overridevirtual

this is the master function for determining the unique output identifier for a job

SilentFile tags should preserve the FULL NAME such that we don't end up with duplicate tags. This will cause problems on BOINC if changed.

Implements protocols::jd2::FileJobOutputter.

Referenced by dump_pose(), and job_has_completed().

void protocols::jd2::RNA_DeNovoJobOutputter::read_done_jobs ( )
private
void protocols::jd2::RNA_DeNovoJobOutputter::set_defaults ( )
private
void protocols::jd2::RNA_DeNovoJobOutputter::set_forced_silent_struct_type ( std::string const &  setting)
void protocols::jd2::RNA_DeNovoJobOutputter::set_silent_file_name ( utility::file::FileName const &  name)

References read_done_jobs(), and silent_file_.

void protocols::jd2::RNA_DeNovoJobOutputter::set_write_no_structures ( bool  value = true)
inline
void protocols::jd2::RNA_DeNovoJobOutputter::set_write_separate_scorefile ( bool  write_separate_scorefile)
void protocols::jd2::RNA_DeNovoJobOutputter::write_all_structs ( )
private

this function is called at the end of job distribution to flush the buffers

References bWriteNoStructures_, core::scoring::pair, saved_structs_, and protocols::jd2::tr().

Referenced by dump_pose(), and flush().

Member Data Documentation

bool protocols::jd2::RNA_DeNovoJobOutputter::bWriteIntermediateFiles_
private

Referenced by other_pose(), and set_defaults().

bool protocols::jd2::RNA_DeNovoJobOutputter::bWriteIntermediateStructures_
private
bool protocols::jd2::RNA_DeNovoJobOutputter::bWriteNoStructures_
private

toggle to switch off writing of structures

Referenced by final_pose(), set_defaults(), set_write_no_structures(), and write_all_structs().

std::string protocols::jd2::RNA_DeNovoJobOutputter::forced_silent_struct_type_
private

override choice of silent_struct_type

Referenced by dump_pose(), set_defaults(), and set_forced_silent_struct_type().

core::Size protocols::jd2::RNA_DeNovoJobOutputter::n_to_buffer_
private

Referenced by dump_pose(), and set_defaults().

core::Real protocols::jd2::RNA_DeNovoJobOutputter::random_flush_frequency_
private

Referenced by dump_pose(), and set_defaults().

utility::vector1< std::pair< core::io::silent::SilentStructOP, utility::file::FileName > > protocols::jd2::RNA_DeNovoJobOutputter::saved_structs_
private
utility::file::FileName protocols::jd2::RNA_DeNovoJobOutputter::silent_file_
private
utility::vector1< std::string > protocols::jd2::RNA_DeNovoJobOutputter::silent_file_tags_
private
bool protocols::jd2::RNA_DeNovoJobOutputter::write_separate_scorefile_
private

whether to write a separate scorefile that contains the scorelines from the silent file

Referenced by final_pose(), and set_write_separate_scorefile().


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