#include <FileJobOutputter.hh>

Inheritance diagram for protocols::jd2::FileJobOutputter:

Public Types
typedef protocols::jd2::JobOutputter	parent

Public Member Functions
	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...

void	final_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag) override=0
	this function outputs the final result of a job. More...

void	other_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false) override=0
	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=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...

std::string	output_name (JobCOP job) override=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 ()
	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
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 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

typedef protocols::jd2::JobOutputter protocols::jd2::FileJobOutputter::parent

Constructor & Destructor Documentation

protocols::jd2::FileJobOutputter::FileJobOutputter ( )

References set_defaults().

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

overridedefault

Member Function Documentation

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

overridevirtual

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 core::conformation::membrane::out, output_name(), and protocols::jd2::TR().

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

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

overridepure virtual

this function outputs the final result of a job.

Implements protocols::jd2::JobOutputter.

Implemented in protocols::features::DatabaseJobOutputter, protocols::jd2::RNA_DeNovoJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::dna::PDBOutput, protocols::jd2::AtomTreeDiffJobOutputter, protocols::jd2::wwPDBJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, and protocols::enzdes::EnzdesJobOutputter.

bool protocols::jd2::FileJobOutputter::job_has_completed ( JobCOP job )

overridepure 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::RNA_DeNovoJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::jd2::wwPDBJobOutputter, protocols::jd2::AtomTreeDiffJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, and protocols::enzdes::EnzdesJobOutputter.

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

overridepure 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::RNA_DeNovoJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::jd2::wwPDBJobOutputter, protocols::jd2::AtomTreeDiffJobOutputter, and protocols::jd2::ScoreOnlyJobOutputter.

std::string protocols::jd2::FileJobOutputter::output_name ( JobCOP job )

overridepure virtual

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

Implements protocols::jd2::JobOutputter.

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

Referenced by file(), and scorefile().

void protocols::jd2::FileJobOutputter::scorefile	(	JobCOP	job,
		core::pose::Pose const &	pose,
		std::string	prefix_tag = `""`,
		std::string	suffix_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::io::raw_data::ScoreMap::add_arbitrary_score_data_from_pose(), core::io::raw_data::ScoreMap::add_arbitrary_string_data_from_pose(), core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(), core::sequence::end, output_name(), scorefile_name_, protocols::jd2::TR(), core::io::raw_data::ScoreFileData::write_pose(), and write_scorefile_.

Referenced by protocols::jd2::ScoreOnlyJobOutputter::final_pose(), protocols::jd2::wwPDBJobOutputter::final_pose(), protocols::jd2::RNA_DeNovoJobOutputter::final_pose(), protocols::jd2::SilentFileJobOutputter::final_pose(), protocols::jd2::ScoreOnlyJobOutputter::other_pose(), protocols::jd2::wwPDBJobOutputter::other_pose(), and protocols::jd2::SilentFileJobOutputter::other_pose().