The ScoreFileOutputter. More...

#include <ScoreFileOutputter.hh>

Inheritance diagram for protocols::jd3::pose_outputters::ScoreFileOutputter:

Public Member Functions
	ScoreFileOutputter ()

	~ScoreFileOutputter () override

std::string	outputter_for_job (utility::tag::TagCOP output_tag, utility::options::OptionCollection const &job_options, InnerLarvalJob const &job) const override
	The ScoreFileOutputter returns the name of the scorefile that it sends its outputs to for this particular job so that the JobQueen can send multiple outputs to the same outputter before invoking flush() More...

std::string	outputter_for_job (PoseOutputSpecification const &spec) const override
	Return an identifier string for the specific instance of the PoseOutputter that ought to be used for a particular job so that the PoseOutputter can e.g. aggregate all of the outputs for a group of jobs and output them all at once when flush is called. The outputter may return the empty string if all outputters (of the same type) are interchangable (e.g. the PDBPoseOutputter). e.g., the SilentFilePoseOutputter returns the name of the file that it sends its outputs to. This function respects the output-filename-suffix that may have been provided by the JobDistributor. More...

PoseOutputSpecificationOP	create_output_specification (LarvalJob const &job, JobOutputIndex const &output_index, utility::options::OptionCollection const &options, utility::tag::TagCOP tag) override
	Using the LarvalJob's job_tag (determined by the (primary) JobOutputter), write extra data about this output Pose to its destination. More...

void	write_output (output::OutputSpecification const &specification, JobResult const &result) override
	Write out the scores for a particular Pose (held in the JobResult) to a score file. More...

void	flush () override
	Output from an outputter may be held back and only flushed when requested by the JobQueen; I/O can be expensive, so it's a good idea to gather up the results of many outputs before flushing them to disk. More...

std::string	class_key () const override
	Return the stiring used by the ScoreFileOutputterCreator for this class. More...

utility::file::FileName	filename_for_job (utility::tag::TagCOP output_tag, utility::options::OptionCollection const &job_options, InnerLarvalJob const &) const

Public Member Functions inherited from protocols::jd3::pose_outputters::SecondaryPoseOutputter
	SecondaryPoseOutputter ()

	~SecondaryPoseOutputter () override

void	determine_job_tag (utility::tag::TagCOP output_tag, utility::options::OptionCollection const &job_options, InnerLarvalJob &job) const final
	This responsibility does not belong in the SecondaryPoseOutputter, so it receives a no-op implementation in the base class – it is primarily the responsibility of the PoseOutputter base class and will not / should not be asked of the SecondaryPoseOutputter. More...

bool	job_has_already_completed (LarvalJob const &job, utility::options::OptionCollection const &options) const final
	This responsibility does not belong in the SecondaryPoseOutputter, so it receives a no-frills implementation in the base class – it is primarily the responsibility of the PoseOutputter base class and will not / should not be asked of the SecondaryPoseOutputter. More...

Public Member Functions inherited from protocols::jd3::pose_outputters::PoseOutputter
	PoseOutputter ()

	~PoseOutputter () override

Public Member Functions inherited from protocols::jd3::output::ResultOutputter
	ResultOutputter ()

	~ResultOutputter () override

Static Public Member Functions
static bool	outputter_specified_by_command_line ()

static std::string	keyname ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static void	list_options_read (utility::options::OptionKeyList &read_options)

Private Attributes
utility::file::FileName	scorefile_name_

utility::vector1< std::string >	scorefile_lines_

Detailed Description

The ScoreFileOutputter.

Constructor & Destructor Documentation

protocols::jd3::pose_outputters::ScoreFileOutputter::ScoreFileOutputter ( )

default

protocols::jd3::pose_outputters::ScoreFileOutputter::~ScoreFileOutputter ( )

override

References flush().

Member Function Documentation

std::string protocols::jd3::pose_outputters::ScoreFileOutputter::class_key ( ) const

overridevirtual

Return the stiring used by the ScoreFileOutputterCreator for this class.

Implements protocols::jd3::pose_outputters::PoseOutputter.

References keyname().

PoseOutputSpecificationOP protocols::jd3::pose_outputters::ScoreFileOutputter::create_output_specification	(	LarvalJob const &	job,
		JobOutputIndex const &	output_index,
		utility::options::OptionCollection const &	options,
		utility::tag::TagCOP	tag
	)

overridevirtual

Using the LarvalJob's job_tag (determined by the (primary) JobOutputter), write extra data about this output Pose to its destination.

Implements protocols::jd3::pose_outputters::PoseOutputter.

References filename_for_job(), protocols::jd3::LarvalJob::inner_job(), protocols::jd3::LarvalJob::job_tag_with_index_suffix(), protocols::jd3::LarvalJob::status_prefix(), and protocols::jd3::LarvalJob::status_suffix().

utility::file::FileName protocols::jd3::pose_outputters::ScoreFileOutputter::filename_for_job	(	utility::tag::TagCOP	output_tag,
		utility::options::OptionCollection const &	job_options,
		InnerLarvalJob const &
	)		const

References protocols::hybridization::path, and protocols::hybridization::score.

Referenced by create_output_specification(), and outputter_for_job().

void protocols::jd3::pose_outputters::ScoreFileOutputter::flush ( )

overridevirtual

Output from an outputter may be held back and only flushed when requested by the JobQueen; I/O can be expensive, so it's a good idea to gather up the results of many outputs before flushing them to disk.

Implements protocols::jd3::output::ResultOutputter.

Referenced by ~ScoreFileOutputter().

std::string protocols::jd3::pose_outputters::ScoreFileOutputter::keyname ( )

static

Referenced by class_key(), protocols::jd3::pose_outputters::ScoreFileOutputterCreator::keyname(), provide_xml_schema(), and protocols::jd3::pose_outputters::ScoreFileOutputSpecification::ScoreFileOutputSpecification().

void protocols::jd3::pose_outputters::ScoreFileOutputter::list_options_read ( utility::options::OptionKeyList & read_options )

static

References protocols::hybridization::path, and protocols::hybridization::score.

Referenced by protocols::jd3::pose_outputters::ScoreFileOutputterCreator::list_options_read().

std::string protocols::jd3::pose_outputters::ScoreFileOutputter::outputter_for_job	(	utility::tag::TagCOP	output_tag,
		utility::options::OptionCollection const &	job_options,
		InnerLarvalJob const &	job
	)		const

overridevirtual

The ScoreFileOutputter returns the name of the scorefile that it sends its outputs to for this particular job so that the JobQueen can send multiple outputs to the same outputter before invoking flush()

Implements protocols::jd3::pose_outputters::PoseOutputter.

References filename_for_job().

std::string protocols::jd3::pose_outputters::ScoreFileOutputter::outputter_for_job ( PoseOutputSpecification const & spec ) const

overridevirtual

Return an identifier string for the specific instance of the PoseOutputter that ought to be used for a particular job so that the PoseOutputter can e.g. aggregate all of the outputs for a group of jobs and output them all at once when flush is called. The outputter may return the empty string if all outputters (of the same type) are interchangable (e.g. the PDBPoseOutputter). e.g., the SilentFilePoseOutputter returns the name of the file that it sends its outputs to. This function respects the output-filename-suffix that may have been provided by the JobDistributor.

Implements protocols::jd3::pose_outputters::PoseOutputter.

bool protocols::jd3::pose_outputters::ScoreFileOutputter::outputter_specified_by_command_line ( )

static

Referenced by protocols::jd3::pose_outputters::ScoreFileOutputterCreator::outputter_specified_by_command_line().

void protocols::jd3::pose_outputters::ScoreFileOutputter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::jd3::pose_outputters::PoseOutputterFactory::complex_type_name_for_secondary_pose_outputter(), and keyname().

Referenced by protocols::jd3::pose_outputters::ScoreFileOutputterCreator::provide_xml_schema().

void protocols::jd3::pose_outputters::ScoreFileOutputter::write_output	(	output::OutputSpecification const &	spec,
		JobResult const &	result
	)

overridevirtual

Write out the scores for a particular Pose (held in the JobResult) to a score file.

Write a pose out to permanent storage (whatever that may be).

currently the score file outputter writes scoress immediately for every output; when it starts to buffer the scoress inside of itself instead,

Implements protocols::jd3::output::ResultOutputter.

References core::io::raw_data::ScoreMap::add_arbitrary_score_data_from_pose(), core::io::raw_data::ScoreMap::add_arbitrary_string_data_from_pose(), and core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose().

Member Data Documentation

utility::vector1< std::string > protocols::jd3::pose_outputters::ScoreFileOutputter::scorefile_lines_

private

utility::file::FileName protocols::jd3::pose_outputters::ScoreFileOutputter::scorefile_name_

private

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

src/protocols/jd3/pose_outputters/ScoreFileOutputter.hh
src/protocols/jd3/pose_outputters/ScoreFileOutputter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation