#include <RNA_DeNovoJobOutputter.hh>

Inheritance diagram for protocols::jd2::RNA_DeNovoJobOutputter:

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Public Types
typedef protocols::jd2::FileJobOutputter	parent

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

Public Member Functions
	RNA_DeNovoJobOutputter ()

	~RNA_DeNovoJobOutputter () override

void	flush () override
	this function flushes any internal buffers - see parent class for explanation More...

void	final_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag) override
	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
	this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. —>these go to file silent_filename+tag 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. More...

std::string	output_name (JobCOP job) override
	this is the master function for determining the unique output identifier for a job More...

std::string	filename (JobCOP) const override

void	set_silent_file_name (utility::file::FileName const &name)

void	set_forced_silent_struct_type (std::string const &)

void	set_write_separate_scorefile (bool write_separate_scorefile)

void	set_write_no_structures (bool value=true)

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	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...

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
core::io::silent::SilentStructOP	dump_pose (utility::file::FileName const &filename, JobCOP job, core::pose::Pose const &pose, bool bWriteScoreOnly, int copy_count=-1, std::string const &suffix="")

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	add_silent_struct (core::io::silent::SilentStructOP ss, utility::file::FileName const &fn)

void	set_defaults ()
	called by the constructor to set filename and options More...

void	read_done_jobs ()

void	write_all_structs ()
	this function is called at the end of job distribution to flush the buffers More...

Private Attributes
bool	bWriteIntermediateFiles_

bool	bWriteIntermediateStructures_

bool	bWriteNoStructures_
	toggle to switch off writing of structures More...

bool	write_separate_scorefile_
	whether to write a separate scorefile that contains the scorelines from the silent file More...

utility::file::FileName	silent_file_

utility::vector1< std::string >	silent_file_tags_

core::Size	n_to_buffer_

core::Real	random_flush_frequency_

utility::vector1< std::pair< core::io::silent::SilentStructOP, utility::file::FileName > >	saved_structs_

std::string	forced_silent_struct_type_
	override choice of silent_struct_type More...

Detailed Description

this is a implementation of JobOutputter for silent-file-based output.

Member Typedef Documentation

◆ parent

typedef protocols::jd2::FileJobOutputter protocols::jd2::RNA_DeNovoJobOutputter::parent

Constructor & Destructor Documentation

◆ RNA_DeNovoJobOutputter()

protocols::jd2::RNA_DeNovoJobOutputter::RNA_DeNovoJobOutputter ( )

References read_done_jobs(), and set_defaults().

◆ ~RNA_DeNovoJobOutputter()

protocols::jd2::RNA_DeNovoJobOutputter::~RNA_DeNovoJobOutputter ( )

override

Member Function Documentation

◆ add_silent_struct()

void protocols::jd2::RNA_DeNovoJobOutputter::add_silent_struct	(	core::io::silent::SilentStructOP	ss,
		utility::file::FileName const &	fn
	)

private

References saved_structs_.

Referenced by dump_pose().

◆ dump_pose()

core::io::silent::SilentStructOP protocols::jd2::RNA_DeNovoJobOutputter::dump_pose	(	utility::file::FileName const &	filename,
		JobCOP	job,
		core::pose::Pose const &	pose,
		bool	bWriteScoreOnly,
		int	copy_count = `-1`,
		std::string const &	suffix = `""`
	)

protected

References protocols::jd2::add_job_data_to_ss(), add_silent_struct(), protocols::jd2::current_replica(), core::pose::Pose::data(), filename(), forced_silent_struct_type_, core::io::silent::SilentStructFactory::get_silent_struct(), n_to_buffer_, output_name(), random_flush_frequency_, core::scoring::rg, saved_structs_, core::pose::datacache::CacheableDataType::SCORE_LINE_STRINGS, protocols::jd2::tr(), and write_all_structs().

Referenced by final_pose(), and other_pose().

◆ filename()

std::string protocols::jd2::RNA_DeNovoJobOutputter::filename ( JobCOP ) const

inlineoverridevirtual

Reimplemented from protocols::jd2::JobOutputter.

References silent_file_.

Referenced by dump_pose(), and other_pose().

◆ final_pose()

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

overridevirtual

this function outputs the final result of a job.

creating output functions/////////////////////////////////////////

Implements protocols::jd2::FileJobOutputter.

References bWriteNoStructures_, protocols::jd2::JobOutputter::call_output_observers(), dump_pose(), protocols::jd2::FileJobOutputter::scorefile(), silent_file_, and write_separate_scorefile_.

◆ flush()

void protocols::jd2::RNA_DeNovoJobOutputter::flush ( )

overridevirtual

this function flushes any internal buffers - see parent class for explanation

Reimplemented from protocols::jd2::JobOutputter.

References write_all_structs().

◆ job_has_completed()

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

overridevirtual

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.

Implements protocols::jd2::FileJobOutputter.

References core::sequence::end, output_name(), core::scoring::pair, read_done_jobs(), saved_structs_, silent_file_tags_, and protocols::jd2::tr().

◆ other_pose()

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

overridevirtual

this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. —>these go to file silent_filename+tag

Implements protocols::jd2::FileJobOutputter.

References bWriteIntermediateFiles_, protocols::jd2::JobOutputter::call_output_observers(), dump_pose(), filename(), and silent_file_.