protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter Class Reference

The DeNovoSilentFilePoseOutputter. More...

#include <DeNovoSilentFilePoseOutputter.hh>

Inheritance diagram for protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter:

Public Member Functions
	DeNovoSilentFilePoseOutputter ()
	~DeNovoSilentFilePoseOutputter () 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...
PoseOutputSpecificationOP	create_output_specification (LarvalJob const &job, JobOutputIndex const &output_index, utility::options::OptionCollection const &job_options, utility::tag::TagCOP tag) override
	Create the PoseOutputSpecification for a particular job. More...
bool	job_has_already_completed (LarvalJob const &job, utility::options::OptionCollection const &options) const override
void	write_output (output::OutputSpecification const &spec, JobResult const &result) override
void	flush () override
	Write out all cached silent files – may happen after an exception is caught by the JobDistributor and the process is about to be spun down. More...
std::string	class_key () const override
	Return the string used by the DeNovoSilentFilePoseOutputterCreator to identify the class in an XML file (which is the string returned by the static keyname method) 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 Member Functions
void	initialize_sf_options (utility::options::OptionCollection const &job_options, utility::tag::TagCOP tag)

Private Attributes
std::string	fname_out_
core::Size	buffer_limit_
core::io::silent::SilentFileOptionsOP	opts_
utility::vector1 < core::io::silent::SilentStructOP >	buffered_structs_
utility::vector1 < core::io::silent::SilentStructOP >	buffered_lores_structs_
bool	dump_ = false

Detailed Description

The DeNovoSilentFilePoseOutputter.

Constructor & Destructor Documentation

protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::DeNovoSilentFilePoseOutputter

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protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::~DeNovoSilentFilePoseOutputter ( )

override

Member Function Documentation

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

overridevirtual

Return the string used by the DeNovoSilentFilePoseOutputterCreator to identify the class in an XML file (which is the string returned by the static keyname method)

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

References keyname().

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

overridevirtual

Create the PoseOutputSpecification for a particular job.

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

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

void protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::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(), and protocols::jd3::InnerLarvalJob::job_tag().

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

overridevirtual

Write out all cached silent files – may happen after an exception is caught by the JobDistributor and the process is about to be spun down.

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

References core::io::silent::SilentFileData::add_structure(), buffered_lores_structs_, buffered_structs_, fname_out_, opts_, and core::io::silent::SilentFileData::write_all().

Referenced by write_output().

void protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::initialize_sf_options ( utility::options::OptionCollection const &  job_options, utility::tag::TagCOP  tag  )

private

References buffer_limit_, dump_, fname_out_, and opts_.

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

overridevirtual

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

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

static

Referenced by class_key(), create_output_specification(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::get_outputter_from_job_tag(), protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator::keyname(), and provide_xml_schema().

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

static

References core::io::silent::SilentFileOptions::list_read_options().

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

std::string protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::outputter_for_job ( utility::tag::TagCOP  sf_tag, utility::options::OptionCollection const &  opts, InnerLarvalJob const &  job  ) const

overridevirtual

If this is just being given an InnerLarvalJob, that means that the outputter is at most a function of the input source–as there's a bijection b/n ILJ and input source. So, let's just use the job_tag. What else can we do?

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

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

static

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

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

static

References core::io::silent::SilentFileOptions::append_attributes_for_tag_parsing(), keyname(), and protocols::jd3::pose_outputters::pose_outputter_xsd_type_definition_w_attributes().

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

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

overridevirtual

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

References core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_base_pairs(), buffer_limit_, buffered_lores_structs_, buffered_structs_, dump_, core::io::pdb::dump_pdb(), flush(), fname_out_, and opts_.

Member Data Documentation

core::Size protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::buffer_limit_

private

Referenced by initialize_sf_options(), and write_output().

utility::vector1< core::io::silent::SilentStructOP > protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::buffered_lores_structs_

private

Referenced by flush(), and write_output().

utility::vector1< core::io::silent::SilentStructOP > protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::buffered_structs_

private

Referenced by flush(), and write_output().

bool protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::dump_ = false

private

Referenced by create_output_specification(), initialize_sf_options(), and write_output().

std::string protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::fname_out_

private

Referenced by flush(), initialize_sf_options(), and write_output().

core::io::silent::SilentFileOptionsOP protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::opts_

private

Referenced by flush(), initialize_sf_options(), and write_output().

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

• src/protocols/jd3/pose_outputters/DeNovoSilentFilePoseOutputter.hh
• src/protocols/jd3/pose_outputters/DeNovoSilentFilePoseOutputter.cc