Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
protocols::jd2::FileJobOutputter Class Reference

#include <FileJobOutputter.hh>

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List of all members.

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).
virtual void final_pose (JobCOP job, core::pose::Pose const &pose)=0
 this function outputs the final result of a job.
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.
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.
virtual std::string output_name (JobCOP job)=0
 this is the master function for determining the unique output identifier for a job
utility::file::FileName const & scorefile_name ()
bool write_scorefile () 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.

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 protocols::jd2::JobOutputter::flush(), 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::enzdes::EnzdesJobOutputter, protocols::features::DatabaseJobOutputter, protocols::jd2::AtomTreeDiffJobOutputter, protocols::jd2::PDBJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, and protocols::jd2::SilentFileJobOutputter.

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::AtomTreeDiffJobOutputter, protocols::jd2::PDBJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, and protocols::jd2::SilentFileJobOutputter.

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 = "" 
) [protected, virtual]

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 FileJobOutputter(), 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]

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