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protocols::jd2::ScoreOnlyJobOutputter Class Reference

#include <ScoreOnlyJobOutputter.hh>

Inheritance diagram for protocols::jd2::ScoreOnlyJobOutputter:
Inheritance graph
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Public Member Functions

 ScoreOnlyJobOutputter ()
 
void final_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag) override
 this function takes a string and writes it to disk (separately from Tracer output). use some sort of extention option system - default .dat? .data? 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. 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...
 
- 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 flush ()
 this function is meant to be redefined in child classes to allow for flushing of memory buffers. Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that the output would be flushed at end of runtime. The original implementation was to A) bend over backward to ensure that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed because it's static) and B) flush the buffers in the destructor. This caused a problem because the buffer-flushing tried to use the Tracers, which had already been destructed...boom crash. More...
 
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...
 
virtual std::string filename (JobCOP) const
 
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...
 

Private Member Functions

void read_done_jobs ()
 

Private Attributes

utility::vector1< std::string > score_file_tags_
 

Additional Inherited Members

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

Detailed Description

Joboutputter that only outputs score files, useful for screening protocols

Constructor & Destructor Documentation

protocols::jd2::ScoreOnlyJobOutputter::ScoreOnlyJobOutputter ( )

References read_done_jobs().

Member Function Documentation

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

this function takes a string and writes it to disk (separately from Tracer output). use some sort of extention option system - default .dat? .data?

this function outputs the final result of a job.

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::call_output_observers(), and protocols::jd2::FileJobOutputter::scorefile().

bool protocols::jd2::ScoreOnlyJobOutputter::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 output_name(), read_done_jobs(), score_file_tags_, and protocols::jd2::TR().

void protocols::jd2::ScoreOnlyJobOutputter::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.

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::call_output_observers(), and protocols::jd2::FileJobOutputter::scorefile().

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

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

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::affixed_numbered_name().

Referenced by job_has_completed().

void protocols::jd2::ScoreOnlyJobOutputter::read_done_jobs ( )
private

Member Data Documentation

utility::vector1< std::string > protocols::jd2::ScoreOnlyJobOutputter::score_file_tags_
private

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