#include <PDBOutput.hh>

Inheritance diagram for protocols::dna::PDBOutput:

Public Types
typedef std::list< std::string >	Strings

typedef std::map< std::string, Strings >	StringsMap

typedef jd2::JobCOP	JobCOP

typedef jd2::JobOP	JobOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef core::pose::PoseCOP	PoseCOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::conformation::Residue	Residue

typedef utility::io::ozstream	ozstream

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

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

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

Public Member Functions
	PDBOutput ()

	~PDBOutput () override

void	final_pose (JobOP, Pose const &, std::string const &) override
	JobDistributor calls this method. More...

void	operator() (Pose const &, std::string const &)
	functor for non-JobDistributor usage More...

void	enabled (bool value) const

bool	enabled () const

void	starting_pose (Pose const &) override
	optionally pass a starting (reference) pose to a JobOutputter for later comparison purposes and/or as interface for initializing evaluators More...

virtual void	reference_pose (Pose const &)

PoseCOP	reference_pose () const

void	score_function (ScoreFunction const &sf)

ScoreFunctionCOP	score_function () const

void	add_info (std::string const &, Strings const &, bool append=true)

bool	remove_info (std::string const &)

void	designed_residue (core::Size, bool value=true)

void	note_designed_residues (PackerTaskCOP)

bool	residues_are_different (Residue const &, Residue const &) const
	compares identity, then internal degrees of freedom for between residues More...

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

	~PDBJobOutputter () override

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

	~wwPDBJobOutputter () 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. This implementation will write a wwPDB-format file (plus scores). It calls a pure virtual so that child classes can write PDB or mmCIF format. 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. This implementation will write a wwPDB-format file (plus scores). It calls a pure virtual so that child classes can write PDB or mmCIF format. 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/cif 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...

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 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	get_residue_indices_to_output ()

void	output_pdb (ozstream &)

void	output_info (ozstream &)

void	output_score_info (ozstream &)

void	output_hbond_info (ozstream &)
	Generates a table of hydrogen bond info and categorizes hbonds by type. More...

void	output_buried_unsatisfied_hbonds (ozstream &)

void	output_design_tags (ozstream &) const

Private Attributes
PoseOP	pose_copy_

PoseCOP	reference_pose_

ScoreFunctionOP	score_function_

core::Real	chi_diff_threshold_

core::Real	mainchain_torsion_diff_threshold_

bool	enabled_

StringsMap	info_map_

utility::vector1< core::Size >	res_indices_to_output_

utility::vector1< bool >	designed_residues_

Additional Inherited Members
Protected Member Functions inherited from protocols::jd2::PDBJobOutputter
void	dump_pose (JobCOP job, core::pose::Pose const &pose, utility::io::ozstream &out, std::string const &filename="") override
	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...

Protected Member Functions inherited from protocols::jd2::wwPDBJobOutputter
virtual std::string	extended_name (JobCOP job, std::string const &suffix="")
	this private function provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb or 1UBQ_0001.cif. More...

virtual std::string	extract_data_from_Job (JobCOP job)
	this function extracts the pose's scores and outputs them as a string to be packaged in an output structure. More...

void	set_path (std::string const &path)
	setter for output file paths, in case child class needs to override -out:path:all with -out:path:[PDB/mmCIF] More...

std::string const &	get_path ()
	getter for output file path More...

void	set_extension (std::string const &extension)
	setter for output file extensions, child class must set More...

std::string const &	get_extension ()
	getter for output file extension More...

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...

Member Typedef Documentation

typedef jd2::JobCOP protocols::dna::PDBOutput::JobCOP

typedef jd2::JobOP protocols::dna::PDBOutput::JobOP

typedef utility::io::ozstream protocols::dna::PDBOutput::ozstream

typedef core::pack::task::PackerTaskCOP protocols::dna::PDBOutput::PackerTaskCOP

typedef core::pose::Pose protocols::dna::PDBOutput::Pose

typedef core::pose::PoseCOP protocols::dna::PDBOutput::PoseCOP

typedef core::pose::PoseOP protocols::dna::PDBOutput::PoseOP

typedef core::conformation::Residue protocols::dna::PDBOutput::Residue

typedef core::scoring::ScoreFunction protocols::dna::PDBOutput::ScoreFunction

typedef core::scoring::ScoreFunctionCOP protocols::dna::PDBOutput::ScoreFunctionCOP

typedef core::scoring::ScoreFunctionCOP protocols::dna::PDBOutput::ScoreFunctionOP

typedef std::list< std::string > protocols::dna::PDBOutput::Strings

typedef std::map< std::string, Strings > protocols::dna::PDBOutput::StringsMap

Constructor & Destructor Documentation

protocols::dna::PDBOutput::PDBOutput ( )

protocols::dna::PDBOutput::~PDBOutput ( )

overridedefault

Member Function Documentation

void protocols::dna::PDBOutput::add_info	(	std::string const &	key,
		Strings const &	info,
		bool	append = `true`
	)

References info_map_.

void protocols::dna::PDBOutput::designed_residue	(	core::Size	index,
		bool	value = `true`
	)

References designed_residues_.

Referenced by note_designed_residues().

void protocols::dna::PDBOutput::enabled ( bool value ) const

inline

References enabled_.

bool protocols::dna::PDBOutput::enabled ( ) const

inline

References enabled_.

void protocols::dna::PDBOutput::final_pose	(	JobOP	job,
		Pose const &	pose,
		std::string const &
	)

overridevirtual

JobDistributor calls this method.

pose is const here, so it must be scored already if score information is expected in output file

Author: ashworth

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::call_output_observers(), enabled_, protocols::jd2::wwPDBJobOutputter::extended_name(), protocols::jd2::wwPDBJobOutputter::extract_data_from_Job(), output_pdb(), and pose_copy_.

void protocols::dna::PDBOutput::get_residue_indices_to_output ( )

private

References core::sequence::end, pose_copy_, reference_pose_, res_indices_to_output_, and residues_are_different().

Referenced by output_pdb().

void protocols::dna::PDBOutput::note_designed_residues ( PackerTaskCOP ptask )

References designed_residue(), and core::sequence::end.

void protocols::dna::PDBOutput::operator()	(	Pose const &	pose,
		std::string const &	name
	)

functor for non-JobDistributor usage

scores pdb

Author: ashworth

References enabled_, protocols::dna::make_subdirs(), output_info(), output_pdb(), and pose_copy_.

void protocols::dna::PDBOutput::output_buried_unsatisfied_hbonds ( ozstream & pdbout )

private

Author: ashworth

References protocols::dna::dna_full_name3(), core::sequence::end, core::pose::metrics::StructureDependentCalculator::get(), core::pose::metrics::EnergyDependentCalculator::get(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_hbond_calc(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_sasa_calc(), pose_copy_, res_indices_to_output_, and protocols::dna::TR().

Referenced by output_pdb().

void protocols::dna::PDBOutput::output_design_tags ( ozstream & pdbout ) const

private

outputs a set of tags describing how residues varied

Author: ashworth

References pose_copy_, reference_pose_, residues_are_different(), and protocols::dna::string_join().

Referenced by output_pdb().

void protocols::dna::PDBOutput::output_hbond_info ( ozstream & pdbout )

private

Generates a table of hydrogen bond info and categorizes hbonds by type.

Author: ashworth

References protocols::comparative_modeling::features::A, protocols::dna::DnaInterfaceFinder::determine_protein_interface(), core::sequence::end, core::chemical::element::F, core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::get_hbe_acc_hybrid(), core::scoring::h2o_hbond, core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::chemical::element::I, core::scoring::hbonds::make_hbBasetoAcc_unitvector(), pose_copy_, res_indices_to_output_, score_function_, and protocols::kinmatch::xyz().

Referenced by output_pdb().

void protocols::dna::PDBOutput::output_info ( ozstream & pdbout )

private

References core::sequence::end, and info_map_.

Referenced by operator()().

void protocols::dna::PDBOutput::output_pdb ( ozstream & pdbout )

private

Author: ashworth

References enabled_, get_residue_indices_to_output(), core::scoring::get_score_function(), output_buried_unsatisfied_hbonds(), output_design_tags(), output_hbond_info(), output_score_info(), pose_copy_, res_indices_to_output_, and score_function_.

Referenced by final_pose(), and operator()().

void protocols::dna::PDBOutput::output_score_info ( ozstream & pdbout )

private

References protocols::comparative_modeling::features::A, protocols::comparative_modeling::features::E, core::sequence::end, core::chemical::element::F, core::chemical::element::I, core::scoring::n_score_types, core::scoring::ScoreTypeManager::name_from_score_type(), pose_copy_, res_indices_to_output_, score_function_, core::scoring::total_score, and core::chemical::element::W.

Referenced by output_pdb().

void protocols::dna::PDBOutput::reference_pose ( Pose const & pose )

virtual

References designed_residues_, and reference_pose_.

pose::PoseCOP protocols::dna::PDBOutput::reference_pose ( ) const

References reference_pose_.

Referenced by starting_pose().

bool protocols::dna::PDBOutput::remove_info ( std::string const & key )

References info_map_.

bool protocols::dna::PDBOutput::residues_are_different	(	Residue const &	res1,
		Residue const &	res2
	)		const

compares identity, then internal degrees of freedom for between residues

References core::conformation::Residue::aa(), core::conformation::Residue::chi(), chi_diff_threshold_, mainchain_torsion_diff_threshold_, core::conformation::Residue::mainchain_torsions(), and core::conformation::Residue::nheavyatoms().

Referenced by get_residue_indices_to_output(), and output_design_tags().

void protocols::dna::PDBOutput::score_function ( ScoreFunction const & sf )

References core::scoring::ScoreFunction::clone(), and score_function_.

ScoreFunctionCOP protocols::dna::PDBOutput::score_function ( ) const

References score_function_.

void protocols::dna::PDBOutput::starting_pose ( Pose const & )

overridevirtual

optionally pass a starting (reference) pose to a JobOutputter for later comparison purposes and/or as interface for initializing evaluators

optionally pass a starting (reference) pose to a JobOutputter for comparison purposes and/or as interface for initializing evaluators. (Currently does nothing in this base class.)

Reimplemented from protocols::jd2::JobOutputter.

References reference_pose().