The PDBPoseOutputter. More...

#include <PDBPoseOutputter.hh>

Inheritance diagram for protocols::jd3::pose_outputters::PDBPoseOutputter:

Public Member Functions
	PDBPoseOutputter ()

	~PDBPoseOutputter () override

void	determine_job_tag (utility::tag::TagCOP output_tag, utility::options::OptionCollection const &job_options, InnerLarvalJob &job) const override
	Determine the inner-larval job's "job_tag" from the <Output> tag / per-job options. More...

std::string	outputter_for_job (utility::tag::TagCOP output_tag, utility::options::OptionCollection const &job_options, InnerLarvalJob const &job) const override

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...

bool	job_has_already_completed (LarvalJob const &job, utility::options::OptionCollection const &options) const override

PoseOutputSpecificationOP	create_output_specification (LarvalJob const &job, JobOutputIndex const &output_index, utility::options::OptionCollection const &options, utility::tag::TagCOP tag) override
	Create the PoseOutputSpecification for a particular job. More...

void	write_output (output::OutputSpecification const &specification, JobResult const &result) override
	Write a pose out to permanent storage (whatever that may be). More...

void	flush () override
	Currently a no-op since the "write output pose" method sends all outputs to disk. More...

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

virtual std::string	output_name (LarvalJob const &job, utility::options::OptionCollection const &options, utility::tag::TagCOP tag) const
	Guess on the name of the output PDB using just the LarvalJob – i.e. in the absence of the JobOutputIndex. More...

virtual std::string	output_name (LarvalJob const &job, JobOutputIndex const &output_index, utility::options::OptionCollection const &options, utility::tag::TagCOP tag) const

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)

Detailed Description

The PDBPoseOutputter.

Constructor & Destructor Documentation

protocols::jd3::pose_outputters::PDBPoseOutputter::PDBPoseOutputter ( )

default

protocols::jd3::pose_outputters::PDBPoseOutputter::~PDBPoseOutputter ( )

overridedefault

Member Function Documentation

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

overridevirtual

Return the stiring used by the PDBPoseOutputterCreator for this class.

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

References keyname().

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

overridevirtual

Create the PoseOutputSpecification for a particular job.

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

References output_name().

void protocols::jd3::pose_outputters::PDBPoseOutputter::determine_job_tag	(	utility::tag::TagCOP	output_tag,
		utility::options::OptionCollection const &	job_options,
		InnerLarvalJob &	job
	)		const

overridevirtual

Determine the inner-larval job's "job_tag" from the <Output> tag / per-job options.

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

References protocols::jd3::InnerLarvalJob::input_tag(), protocols::jd3::InnerLarvalJob::job_tag(), and keyname().

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

overridevirtual

Currently a no-op since the "write output pose" method sends all outputs to disk.

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

bool protocols::jd3::pose_outputters::PDBPoseOutputter::job_has_already_completed	(	LarvalJob const &	job,
		utility::options::OptionCollection const &	options
	)		const

overridevirtual

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

References protocols::abinitio::filename(), protocols::jd3::LarvalJob::inner_job(), keyname(), output_name(), and protocols::jd3::pose_outputters::TR().

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

static

Referenced by class_key(), determine_job_tag(), protocols::jd3::standard::StandardJobQueen::get_outputter_from_job_tag(), job_has_already_completed(), protocols::jd3::pose_outputters::PDBPoseOutputterCreator::keyname(), output_name(), protocols::jd3::pose_outputters::PDBPoseOutputSpecification::PDBPoseOutputSpecification(), and provide_xml_schema().

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

static

References core::io::StructFileRepOptions::list_options_read(), and protocols::hybridization::path.

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

std::string protocols::jd3::pose_outputters::PDBPoseOutputter::output_name	(	LarvalJob const &	job,
		utility::options::OptionCollection const &	options,
		utility::tag::TagCOP	tag
	)		const

virtual

Guess on the name of the output PDB using just the LarvalJob – i.e. in the absence of the JobOutputIndex.

Public for testing

References protocols::jd3::JobOutputIndex::n_primary_outputs, protocols::jd3::LarvalJob::nstruct_index(), protocols::jd3::LarvalJob::nstruct_max(), and protocols::jd3::JobOutputIndex::primary_output_index.

Referenced by create_output_specification(), and job_has_already_completed().

std::string protocols::jd3::pose_outputters::PDBPoseOutputter::output_name	(	LarvalJob const &	job,
		JobOutputIndex const &	output_index,
		utility::options::OptionCollection const &	options,
		utility::tag::TagCOP	tag
	)		const

virtual

Public for testing

Reimplemented in protocols::jd3::pose_outputters::mmTFPoseOutputter.

References protocols::jd3::LarvalJob::job_tag_with_index_suffix(), keyname(), protocols::hybridization::path, and protocols::jd3::LarvalJob::status_prefix().

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

overridevirtual

In returning the empty string, we signal to the JobQueen (or any other user) that all PDBPoseOutputters are interchangable – that they do not buffer data destined for a single file, and so a single PDBPoseOutputter may be used for all output Poses.

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

std::string protocols::jd3::pose_outputters::PDBPoseOutputter::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::PDBPoseOutputter::outputter_specified_by_command_line ( )

static

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

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

static

References keyname(), and protocols::jd3::pose_outputters::pose_outputter_xsd_type_definition_w_attributes().

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