for now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb More...

#include <EnzdesJobOutputter.hh>

Public Types
typedef protocols::jd2::PDBJobOutputter	parent

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

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

Public Member Functions
	EnzdesJobOutputter ()

	~EnzdesJobOutputter ()

void	final_pose (protocols::jd2::JobOP 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...

bool	job_has_completed (protocols::jd2::JobOP job)

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

virtual	~PDBJobOutputter ()

virtual void	other_pose (JobOP 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

void	call_output_observers (core::pose::Pose const &pose, JobOP job) const
	call all output_observers More...

void	add_output_observer (JobOutputterObserverAP an_observer)

void	remove_output_observer (JobOutputterObserverAP old_observer)

Protected Member Functions
void	scorefile (protocols::jd2::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::PDBJobOutputter
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...

std::string	extended_name (JobCOP job, std::string const &suffix)

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::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
core::io::silent::SilentFileDataOP	scorefile_writer_

protocols::enzdes::EnzdesScorefileFilterOP	enz_scofile_

bool	silent_output_

protocols::jd2::SilentFileJobOutputterOP	silent_job_outputter_

Detailed Description

for now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb

Member Typedef Documentation

typedef protocols::jd2::PDBJobOutputter protocols::enzdes::EnzdesJobOutputter::parent

Constructor & Destructor Documentation

protocols::enzdes::EnzdesJobOutputter::EnzdesJobOutputter ( )

References enz_scofile_, utility::file::file_delete(), utility::file::file_exists(), basic::options::OptionKeys::out::file::o, basic::options::option, basic::options::OptionKeys::out::overwrite, protocols::jd2::FileJobOutputter::scorefile_name(), scorefile_writer_, silent_job_outputter_, silent_output_, basic::options::OptionKeys::out::file::silent_struct_type, user, and protocols::jd2::FileJobOutputter::write_scorefile().

protocols::enzdes::EnzdesJobOutputter::~EnzdesJobOutputter ( )

Member Function Documentation

void protocols::enzdes::EnzdesJobOutputter::final_pose	(	protocols::jd2::JobOP	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).

Reimplemented from protocols::jd2::PDBJobOutputter.

References protocols::jd2::PDBJobOutputter::final_pose(), scorefile(), silent_job_outputter_, and silent_output_.

bool protocols::enzdes::EnzdesJobOutputter::job_has_completed ( protocols::jd2::JobOP job )

References protocols::jd2::PDBJobOutputter::job_has_completed(), silent_job_outputter_, and silent_output_.

void protocols::enzdes::EnzdesJobOutputter::scorefile	(	protocols::jd2::JobCOP	job,
		core::pose::Pose const &	pose,
		std::string	tag = `""`,
		std::string	scorefile = `""`
	)

protectedvirtual

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.

Reimplemented from protocols::jd2::FileJobOutputter.

References utility::io::ozstream::close(), basic::options::OptionKeys::enzdes::dump_final_repack_without_ligand_pdb, protocols::jd2::PDBJobOutputter::dump_pose(), enz_scofile_, basic::options::OptionKeys::enzdes::final_repack_without_ligand, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), utility::io::ozstream::good(), basic::options::option, out, protocols::jd2::PDBJobOutputter::output_name(), protocols::jd2::FileJobOutputter::scorefile_name(), scorefile_writer_, ss, utility_exit_with_message, and protocols::jd2::FileJobOutputter::write_scorefile().