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protocols::jd2::mmCIFJobOutputter Class Reference

#include <mmCIFJobOutputter.hh>

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

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

Public Member Functions

 mmCIFJobOutputter ()
 
 ~mmCIFJobOutputter () override
 
- Public Member Functions inherited from protocols::jd2::wwPDBJobOutputter
 wwPDBJobOutputter ()
 
 ~wwPDBJobOutputter () override
 
void final_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag) override
 this function outputs the final result of a job. This implementation will write a wwPDB-format file (plus scores). It calls a pure virtual so that child classes can write PDB or mmCIF format. 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. This implementation will write a wwPDB-format file (plus scores). It calls a pure virtual so that child classes can write PDB or mmCIF format. 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. The base implementation looks for a pdb/cif with the job's name already in existence. 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...
 

Protected Member Functions

void dump_pose (JobCOP job, core::pose::Pose const &pose, utility::io::ozstream &out, std::string const &filename="") override
 this function outputs the final result of a job. This implementation will write a mmCIF file (plus scores). More...
 
- Protected Member Functions inherited from protocols::jd2::wwPDBJobOutputter
virtual std::string extended_name (JobCOP job, std::string const &suffix="")
 this private function provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb or 1UBQ_0001.cif. More...
 
virtual std::string extract_data_from_Job (JobCOP job)
 this function extracts the pose's scores and outputs them as a string to be packaged in an output structure. More...
 
void set_path (std::string const &path)
 setter for output file paths, in case child class needs to override -out:path:all with -out:path:[PDB/mmCIF] More...
 
std::string const & get_path ()
 getter for output file path More...
 
void set_extension (std::string const &extension)
 setter for output file extensions, child class must set More...
 
std::string const & get_extension ()
 getter for output file extension More...
 
- 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 dump_extra_data_file (JobCOP job, std::string const &parent_filename)
 
void dump_energies_file (core::io::StructFileRepCOP sfr, std::string const &parent_filename)
 

Private Attributes

std::string extension_
 

Detailed Description

outputs mmCIFs and associated files, uncompressed.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::jd2::mmCIFJobOutputter::mmCIFJobOutputter ( )
protocols::jd2::mmCIFJobOutputter::~mmCIFJobOutputter ( )
overridedefault

Member Function Documentation

void protocols::jd2::mmCIFJobOutputter::dump_energies_file ( core::io::StructFileRepCOP  sfr,
std::string const &  parent_filename 
)
private

this function takes energies associated with the pose and writes it to JOBNAME.energies. Filename is the location the parent mmCIF got written to. It's pretty stupid to do that via this string instead of the Job object, given that that's the Job object's purpose, but otherwise we lose the "tag" ability specified several layers up in wwPDBJO. tagging_filename is filename from dump_pose, passaged for extract_scores further along.

this function takes energies from the pose and writes it to JOBNAME.energies

References core::conformation::membrane::out, core::io::pose_data_cache_from_sfr(), and core::io::pose_energies_from_sfr().

Referenced by dump_pose().

void protocols::jd2::mmCIFJobOutputter::dump_extra_data_file ( JobCOP  job,
std::string const &  parent_filename 
)
private

this function takes "extra data" associated with the job and writes it to JOBNAME.extradata. Filename is the location the parent mmCIF got written to. It's pretty stupid to do that via this string instead of the Job object, given that that's the Job object's purpose, but otherwise we lose the "tag" ability specified several layers up in wwPDBJO.

this function takes "extra data" associated with the job and writes it to JOBNAME.extradata

References protocols::jd2::wwPDBJobOutputter::extract_data_from_Job(), and core::conformation::membrane::out.

Referenced by dump_pose().

void protocols::jd2::mmCIFJobOutputter::dump_pose ( JobCOP  job,
core::pose::Pose const &  pose,
utility::io::ozstream &  out,
std::string const &  filename = "" 
)
overrideprotectedvirtual

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

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 mmCIF file (plus scores). 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 an mmCIF with the job's name already in existence. this is the master function for determining the unique output identifier for a job this private function provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.cif. In this case the extension is .cif

Refactored (in PDBJobOutputter) in the 2016 Chemical XRW (eXtreme Rosetta Workshop) by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Parameters
[in]jobConst-access owning pointer to the job from which the data will be extracted.
[out]data_outA string in which the data will be stored, that can later be passed to whatever container wants it. protected mmCIF output///////////////////////////////////// This is the function actually different between mmCIF and PDB output, and unshared by the wwPDB parent class. Here it causes a cif file to be written. Pure virtual in the base class. filename is an optional label for the score data table, not an actual control.

private function (just prevents code duplication) to fill ozstream

Implements protocols::jd2::wwPDBJobOutputter.

References core::io::mmcif::dump_cif(), dump_energies_file(), dump_extra_data_file(), and protocols::jd2::JobOutputter::filename().

Member Data Documentation

std::string protocols::jd2::mmCIFJobOutputter::extension_
private

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