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protocols::jd2::FileJobOutputter Class Referenceabstract

#include <FileJobOutputter.hh>

Inheritance diagram for protocols::jd2::FileJobOutputter:
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Public Types

typedef
protocols::jd2::JobOutputter 
parent
 

Public Member Functions

 FileJobOutputter ()
 
virtual ~FileJobOutputter ()
 
virtual void file (JobCOP job, std::string const &data)
 this function takes a string and writes it to disk (separately from Tracer output). More...
 
virtual void final_pose (JobCOP job, core::pose::Pose const &pose)=0
 this function outputs the final result of a job. More...
 
virtual void other_pose (JobCOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false)=0
 this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. More...
 
virtual bool job_has_completed (JobCOP job)=0
 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. The base implementation looks for a pdb with the job's name already in existence. More...
 
virtual std::string output_name (JobCOP job)=0
 this is the master function for determining the unique output identifier for a job More...
 
utility::file::FileName const & scorefile_name ()
 
bool write_scorefile () const
 
- Public Member Functions inherited from protocols::jd2::JobOutputter
 JobOutputter ()
 
virtual ~JobOutputter ()
 
virtual void flush ()
 this function is meant to be redefined in child classes to allow for flushing of memory buffers. 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
 

Protected Member Functions

virtual void scorefile (JobCOP job, core::pose::Pose const &pose, std::string 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 provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb More...
 

Private Attributes

bool write_scorefile_
 this function will handle the scorefile for arbitrary poses. More...
 
utility::file::FileName scorefile_name_
 

Detailed Description

this is a middle-layer implementation of JobOutputter for file-based output. It handles scorefile output, as scorefiles are common to file-outputting methods.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::jd2::FileJobOutputter::FileJobOutputter ( )
protocols::jd2::FileJobOutputter::~FileJobOutputter ( )
virtual

Member Function Documentation

void protocols::jd2::FileJobOutputter::file ( JobCOP  job,
std::string const &  data 
)
virtual

this function takes a string and writes it to disk (separately from Tracer output).

this base class implementation will try to append whatever string it gets to a file named after the job, with a user-specified suffix.

Implements protocols::jd2::JobOutputter.

References output_name(), and protocols::jd2::TR().

Referenced by protocols::jd2::PDBJobOutputter::other_pose().

virtual void protocols::jd2::FileJobOutputter::final_pose ( JobCOP  job,
core::pose::Pose const &  pose 
)
pure virtual
virtual bool protocols::jd2::FileJobOutputter::job_has_completed ( JobCOP  job)
pure virtual

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. The base implementation looks for a pdb with the job's name already in existence.

Implements protocols::jd2::JobOutputter.

Implemented in protocols::features::DatabaseJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::jd2::PDBJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, protocols::jd2::AtomTreeDiffJobOutputter, and protocols::enzdes::EnzdesJobOutputter.

virtual void protocols::jd2::FileJobOutputter::other_pose ( JobCOP  job,
core::pose::Pose const &  pose,
std::string const &  tag,
int  copy_count = -1,
bool  score_only = false 
)
pure virtual

this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.

Implements protocols::jd2::JobOutputter.

Implemented in protocols::features::DatabaseJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::jd2::PDBJobOutputter, protocols::jd2::AtomTreeDiffJobOutputter, and protocols::jd2::ScoreOnlyJobOutputter.

virtual std::string protocols::jd2::FileJobOutputter::output_name ( JobCOP  job)
pure virtual
void protocols::jd2::FileJobOutputter::scorefile ( JobCOP  job,
core::pose::Pose const &  pose,
std::string  tag = "",
std::string  scorefile = "" 
)
protectedvirtual

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.

Reimplemented in protocols::enzdes::EnzdesJobOutputter.

References core::sequence::end, protocols::jd2::ScoreMap::score_map_from_scored_pose(), protocols::jd2::TR(), and core::io::raw_data::ScoreFileData::write_pose().

Referenced by protocols::jd2::ScoreOnlyJobOutputter::final_pose(), protocols::jd2::PDBJobOutputter::final_pose(), protocols::jd2::ScoreOnlyJobOutputter::other_pose(), and protocols::jd2::PDBJobOutputter::other_pose().

utility::file::FileName const& protocols::jd2::FileJobOutputter::scorefile_name ( )
inline
bool protocols::jd2::FileJobOutputter::write_scorefile ( ) const
inline

Member Data Documentation

utility::file::FileName protocols::jd2::FileJobOutputter::scorefile_name_
private

Referenced by FileJobOutputter(), and scorefile_name().

bool protocols::jd2::FileJobOutputter::write_scorefile_
private

this function will handle the scorefile for arbitrary poses.

Referenced by FileJobOutputter(), and write_scorefile().


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