#include <PDBJobOutputter.hh>

Inheritance diagram for protocols::jd2::PDBJobOutputter:

Collaboration diagram for protocols::jd2::PDBJobOutputter:

Public Types
typedef protocols::jd2::FileJobOutputter	parent

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

Public Member Functions
	PDBJobOutputter ()

virtual	~PDBJobOutputter ()

virtual void	final_pose (JobCOP job, core::pose::Pose const &pose)
	this function takes a string and writes it to disk (separately from Tracer output). This implementation writes a single file whose filename is based on the job and a user-specified extension (default .data) More...

virtual void	other_pose (JobCOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false)
	this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. This implementation will write a PDB file (plus scores). More...

virtual bool	job_has_completed (JobCOP job)
	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...

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

Public Member Functions inherited from protocols::jd2::FileJobOutputter
	FileJobOutputter ()

virtual	~FileJobOutputter ()

virtual void	file (JobCOP job, std::string const &data)
	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 ()

virtual	~JobOutputter ()

virtual void	flush ()
	this function is meant to be redefined in child classes to allow for flushing of memory buffers. 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

Protected Member Functions
virtual std::string	extended_name (JobCOP job)
	this private function provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb. In this case the extension is .pdb More...

virtual void	extract_scores (core::pose::Pose const &pose, utility::io::ozstream &out)
	this function extracts the pose's scores for printing More...

virtual void	extract_data_from_Job (JobCOP job, utility::io::ozstream &out)
	this function extracts the pose's scores for printing More...

virtual void	dump_pose (JobCOP job, core::pose::Pose const &pose, utility::io::ozstream &out)
	handles ozstream output; shared by both pdb output functions More...

Protected Member Functions inherited from protocols::jd2::FileJobOutputter
virtual void	scorefile (JobCOP job, core::pose::Pose const &pose, std::string 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 provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb More...

Private Attributes
std::string	extension_

std::string	path_

Detailed Description

this simplest implementation of JobOutputter outputs raw PDBs and associated files, uncompressed.

Member Typedef Documentation

typedef protocols::jd2::FileJobOutputter protocols::jd2::PDBJobOutputter::parent

Constructor & Destructor Documentation

protocols::jd2::PDBJobOutputter::PDBJobOutputter ( )

References extension_, path_, and protocols::jd2::TR().

Referenced by protocols::jd2::PDBJobOutputterCreator::create_JobOutputter().

protocols::jd2::PDBJobOutputter::~PDBJobOutputter ( )

virtual

Member Function Documentation

void protocols::jd2::PDBJobOutputter::dump_pose	(	JobCOP	job,
		core::pose::Pose const &	pose,
		utility::io::ozstream &	out
	)

protectedvirtual

handles ozstream output; shared by both pdb output functions

protected PDB output/////////////////////////////////////

private function (just prevents code duplication) to fill ozstream

References core::io::pdb::FileData::dump_pdb(), extract_data_from_Job(), and extract_scores().

Referenced by final_pose(), other_pose(), and protocols::enzdes::EnzdesJobOutputter::scorefile().

std::string protocols::jd2::PDBJobOutputter::extended_name ( JobCOP job)

protectedvirtual

this private function provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb. In this case the extension is .pdb

References extension_, and output_name().

Referenced by protocols::dna::PDBOutput::final_pose(), final_pose(), job_has_completed(), and other_pose().

void protocols::jd2::PDBJobOutputter::extract_data_from_Job	(	JobCOP	job,
		utility::io::ozstream &	out
	)

protectedvirtual

this function extracts the pose's scores for printing

References core::sequence::end.

Referenced by dump_pose(), and protocols::dna::PDBOutput::final_pose().

void protocols::jd2::PDBJobOutputter::extract_scores	(	core::pose::Pose const &	pose,
		utility::io::ozstream &	out
	)

protectedvirtual

this function extracts the pose's scores for printing

In order for this to work as expected, the Pose's cached energies must match up with the (current) conformation. A good time to do this is at the end of your protocol's apply() method: scorefxn( pose );

References core::io::pdb::extract_scores().

Referenced by dump_pose().

void protocols::jd2::PDBJobOutputter::final_pose	(	JobCOP	job,
		core::pose::Pose const &	pose
	)

virtual

this function takes a string and writes it to disk (separately from Tracer output). This implementation writes a single file whose filename is based on the job and a user-specified extension (default .data)

this function outputs the final result of a job. This implementation will write a PDB file (plus scores).

Implements protocols::jd2::FileJobOutputter.

Reimplemented in protocols::dna::PDBOutput, and protocols::enzdes::EnzdesJobOutputter.

References dump_pose(), extended_name(), path_, protocols::jd2::FileJobOutputter::scorefile(), and protocols::jd2::TR().

Referenced by protocols::enzdes::EnzdesJobOutputter::final_pose().

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

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::FileJobOutputter.

Reimplemented in protocols::enzdes::EnzdesJobOutputter.

References extended_name(), protocols::swa::rna::file_exists(), and path_.

Referenced by protocols::enzdes::EnzdesJobOutputter::job_has_completed().

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

virtual

this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. This implementation will write a PDB file (plus scores).

Implements protocols::jd2::FileJobOutputter.

References dump_pose(), extended_name(), protocols::jd2::FileJobOutputter::file(), protocols::jd2::FileJobOutputter::scorefile(), and protocols::jd2::TR().

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

virtual

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

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::affixed_numbered_name().

Referenced by extended_name(), and protocols::enzdes::EnzdesJobOutputter::scorefile().