#include <AtomTreeDiffJobOutputter.hh>

Inheritance diagram for protocols::jd2::AtomTreeDiffJobOutputter:

Public Member Functions
	AtomTreeDiffJobOutputter ()

	~AtomTreeDiffJobOutputter () override

void	final_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag) override
	this function outputs the final result of a job. More...

void	other_pose (JobOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false) override
	this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. More...

bool	job_has_completed (JobCOP job) override
	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...

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

void	set_precision (int bb_precision, int sc_precision, int bondlen_precision)
	what precision should the atom_tree_diff be ouput at? More...

void	use_input_for_ref (bool use_input=true)
	use input as reference pose? More...

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

	~FileJobOutputter () override

void	set_defaults ()

void	file (JobCOP job, std::string const &data) override
	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 ()
	constructor – reads cmd-line to initialize evaluators More...

	~JobOutputter () override

virtual void	flush ()
	this function is meant to be redefined in child classes to allow for flushing of memory buffers. Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that the output would be flushed at end of runtime. The original implementation was to A) bend over backward to ensure that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed because it's static) and B) flush the buffers in the destructor. This caused a problem because the buffer-flushing tried to use the Tracers, which had already been destructed...boom crash. 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	set_defaults ()
	clear the list of evaluators More...

Private Member Functions
void	dump_pose (std::string const &tag, core::pose::Pose const &pose, std::map< std::string, core::Real > scores, JobCOP job)
	Appends pose to the silent file. More...

Private Attributes
utility::io::ozstream	out_

std::string	outfile_name_

std::set< std::string >	used_tags_

std::string	last_ref_tag_

core::pose::Pose	last_ref_pose_

core::import_pose::atom_tree_diffs::AtomTreeDiff	atom_tree_diff_

int	bb_precision_
	precision to output atom tree diff at. More...

int	sc_precision_

int	bondlen_precision_

bool	use_input_
	use input as reference pose? (default false) More...

Additional Inherited Members
Public Types inherited from protocols::jd2::FileJobOutputter
typedef protocols::jd2::JobOutputter	parent

Protected Member Functions inherited from protocols::jd2::FileJobOutputter
virtual void	scorefile (JobCOP job, core::pose::Pose const &pose, std::string prefix_tag="", std::string suffix_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 generates the affixed, numbered name for the job as prefix + input + suffix + number (affixes from options system). This function is deliberately not virtual, this should be a common mechanism; your JobOutputter can not call it if it would like. More...

Detailed Description

this is a middle-layer implementation of JobOutputter for file-based output. It handles scorefile output, as scorefiles are common to file-outputting methods.

Constructor & Destructor Documentation

protocols::jd2::AtomTreeDiffJobOutputter::AtomTreeDiffJobOutputter ( )

References outfile_name_, protocols::hybridization::path, and set_precision().

protocols::jd2::AtomTreeDiffJobOutputter::~AtomTreeDiffJobOutputter ( )

overridedefault

Member Function Documentation

void protocols::jd2::AtomTreeDiffJobOutputter::dump_pose	(	std::string const &	tag,
		core::pose::Pose const &	pose,
		std::map< std::string, core::Real >	scores,
		JobCOP	job
	)

private

Appends pose to the silent file.

Appends pose to atom tree diff file.

References bb_precision_, bondlen_precision_, core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::import_pose::atom_tree_diffs::dump_reference_pose(), core::sequence::end, last_ref_pose_, last_ref_tag_, out_, outfile_name_, sc_precision_, protocols::jd2::TR(), use_input_, and used_tags_.

Referenced by final_pose().

void protocols::jd2::AtomTreeDiffJobOutputter::final_pose	(	JobOP	job,
		core::pose::Pose const &	pose,
		std::string const &	tag
	)

overridevirtual

this function outputs the final result of a job.

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::call_output_observers(), dump_pose(), core::sequence::end, and output_name().

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

overridevirtual

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.

References output_name(), and used_tags_.

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