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protocols::enzdes::EnzdesJobOutputter Class Reference

for now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb More...

#include <EnzdesJobOutputter.hh>

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Public Types

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

Public Member Functions

 EnzdesJobOutputter ()
 
 ~EnzdesJobOutputter ()
 
void final_pose (protocols::jd2::JobCOP job, core::pose::Pose const &pose)
 this function takes a string and writes it to disk (separately from Tracer output). This implementation writes a single file whose filename is based on the job and a user-specified extension (default .data) More...
 
bool job_has_completed (protocols::jd2::JobCOP job)
 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...
 
- Public Member Functions inherited from protocols::jd2::PDBJobOutputter
 PDBJobOutputter ()
 
virtual ~PDBJobOutputter ()
 
virtual void other_pose (JobCOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false)
 this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. This implementation will write a PDB file (plus scores). More...
 
virtual std::string output_name (JobCOP job)
 this is the master function for determining the unique output identifier for a job More...
 
- Public Member Functions inherited from protocols::jd2::FileJobOutputter
 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...
 
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

void scorefile (protocols::jd2::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::PDBJobOutputter
virtual std::string extended_name (JobCOP job)
 this private function provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb. In this case the extension is .pdb More...
 
virtual void extract_scores (core::pose::Pose const &pose, utility::io::ozstream &out)
 this function extracts the pose's scores for printing More...
 
virtual void extract_data_from_Job (JobCOP job, utility::io::ozstream &out)
 this function extracts the pose's scores for printing More...
 
virtual void dump_pose (JobCOP job, core::pose::Pose const &pose, utility::io::ozstream &out)
 handles ozstream output; shared by both pdb output functions More...
 

Private Attributes

core::io::silent::SilentFileDataOP scorefile_writer_
 
protocols::enzdes::EnzdesScorefileFilterOP enz_scofile_
 
bool silent_output_
 
protocols::jd2::SilentFileJobOutputterOP silent_job_outputter_
 

Detailed Description

for now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::enzdes::EnzdesJobOutputter::EnzdesJobOutputter ( )
protocols::enzdes::EnzdesJobOutputter::~EnzdesJobOutputter ( )

Member Function Documentation

void protocols::enzdes::EnzdesJobOutputter::final_pose ( protocols::jd2::JobCOP  job,
core::pose::Pose const &  pose 
)
virtual

this function takes a string and writes it to disk (separately from Tracer output). This implementation writes a single file whose filename is based on the job and a user-specified extension (default .data)

this function outputs the final result of a job. This implementation will write a PDB file (plus scores).

Reimplemented from protocols::jd2::PDBJobOutputter.

References protocols::jd2::PDBJobOutputter::final_pose(), scorefile(), silent_job_outputter_, and silent_output_.

bool protocols::enzdes::EnzdesJobOutputter::job_has_completed ( protocols::jd2::JobCOP  job)
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.

Reimplemented from protocols::jd2::PDBJobOutputter.

References protocols::jd2::PDBJobOutputter::job_has_completed(), silent_job_outputter_, and silent_output_.

void protocols::enzdes::EnzdesJobOutputter::scorefile ( protocols::jd2::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 from protocols::jd2::FileJobOutputter.

References protocols::jd2::PDBJobOutputter::dump_pose(), enz_scofile_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::jd2::PDBJobOutputter::output_name(), protocols::jd2::FileJobOutputter::scorefile_name(), scorefile_writer_, and protocols::jd2::FileJobOutputter::write_scorefile().

Referenced by final_pose().

Member Data Documentation

protocols::enzdes::EnzdesScorefileFilterOP protocols::enzdes::EnzdesJobOutputter::enz_scofile_
private

Referenced by EnzdesJobOutputter(), and scorefile().

core::io::silent::SilentFileDataOP protocols::enzdes::EnzdesJobOutputter::scorefile_writer_
private

Referenced by EnzdesJobOutputter(), and scorefile().

protocols::jd2::SilentFileJobOutputterOP protocols::enzdes::EnzdesJobOutputter::silent_job_outputter_
private
bool protocols::enzdes::EnzdesJobOutputter::silent_output_
private

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