#include <PDBOutput.hh>

Inheritance diagram for protocols::dna::PDBOutput:

Collaboration 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 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::FileJobOutputter	parent

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

Public Member Functions
	PDBOutput ()

virtual	~PDBOutput ()

virtual void	final_pose (JobCOP, Pose const &)
	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

virtual void	starting_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 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 ()

virtual	~PDBJobOutputter ()

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 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

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

Additional Inherited Members
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...

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...

Detailed Description

Definition at line 37 of file PDBOutput.hh.

Member Typedef Documentation

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

Definition at line 41 of file PDBOutput.hh.

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

Definition at line 50 of file PDBOutput.hh.

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

Definition at line 48 of file PDBOutput.hh.

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

Definition at line 42 of file PDBOutput.hh.

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

Definition at line 44 of file PDBOutput.hh.

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

Definition at line 43 of file PDBOutput.hh.

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

Definition at line 49 of file PDBOutput.hh.

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

Definition at line 45 of file PDBOutput.hh.

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

Definition at line 47 of file PDBOutput.hh.

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

Definition at line 46 of file PDBOutput.hh.

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

Definition at line 39 of file PDBOutput.hh.

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

Definition at line 40 of file PDBOutput.hh.

Constructor & Destructor Documentation

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

Definition at line 78 of file PDBOutput.cc.

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

virtual

Definition at line 87 of file PDBOutput.cc.

Member Function Documentation

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

Definition at line 210 of file PDBOutput.cc.

References protocols::simple_moves::append, core::sequence::end, and info_map_.

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

Definition at line 167 of file PDBOutput.cc.

References designed_residues_.

Referenced by note_designed_residues().

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

inline

Definition at line 60 of file PDBOutput.hh.

References enabled_.

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

inline

Definition at line 61 of file PDBOutput.hh.

References enabled_.

void protocols::dna::PDBOutput::final_pose	(	JobCOP	job,
		Pose const &	pose
	)

virtual

JobDistributor calls this method.

PDBOutput::final_pose

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

Author: ashworth

Reimplemented from protocols::jd2::PDBJobOutputter.

Definition at line 94 of file PDBOutput.cc.

References enabled_, protocols::jd2::PDBJobOutputter::extended_name(), protocols::jd2::PDBJobOutputter::extract_data_from_Job(), output_pdb(), and pose_copy_.

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

private

Definition at line 271 of file PDBOutput.cc.

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)

Definition at line 182 of file PDBOutput.cc.

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

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

functor for non-JobDistributor usage

PDBOutput () operator – non-JobDistributor usage

scores pdb

Author: ashworth

Definition at line 113 of file PDBOutput.cc.

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

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

private

output_buried_unsatisfied_hbonds

Author: ashworth

Definition at line 532 of file PDBOutput.cc.

References protocols::dna::dna_full_name3(), core::sequence::end, core::pose::metrics::StructureDependentCalculator::get(), core::pose::metrics::EnergyDependentCalculator::get(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_hbond_calc(), protocols::toolbox::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

output design tags

outputs a set of tags describing how residues varied

Author: ashworth

Definition at line 306 of file PDBOutput.cc.

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.

output_hbond_info

Author: ashworth

Definition at line 412 of file PDBOutput.cc.

References protocols::comparative_modeling::features::A, protocols::dna::DnaInterfaceFinder::determine_protein_interface(), core::sequence::end, 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::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

Definition at line 194 of file PDBOutput.cc.

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

Referenced by operator()().

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

private

PDBOutput::output_pdb

Author: ashworth

Definition at line 135 of file PDBOutput.cc.

References enabled_, get_residue_indices_to_output(), core::scoring::getScoreFunction(), 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

Definition at line 342 of file PDBOutput.cc.

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

Referenced by output_pdb().

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

virtual

Definition at line 153 of file PDBOutput.cc.

References designed_residues_, and reference_pose_.

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

Definition at line 159 of file PDBOutput.cc.

References reference_pose_.

Referenced by starting_pose().

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

Definition at line 228 of file PDBOutput.cc.

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

Definition at line 238 of file PDBOutput.cc.

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)

Definition at line 161 of file PDBOutput.cc.

References score_function_.

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

Definition at line 165 of file PDBOutput.cc.

References score_function_.

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

virtual

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.

Definition at line 151 of file PDBOutput.cc.

References reference_pose().

Member Data Documentation

core::Real protocols::dna::PDBOutput::chi_diff_threshold_

private

Definition at line 90 of file PDBOutput.hh.

Referenced by residues_are_different().

utility::vector1< bool > protocols::dna::PDBOutput::designed_residues_

private

Definition at line 94 of file PDBOutput.hh.

Referenced by designed_residue(), and reference_pose().

bool protocols::dna::PDBOutput::enabled_

mutableprivate

Definition at line 91 of file PDBOutput.hh.

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

StringsMap protocols::dna::PDBOutput::info_map_

private

Definition at line 92 of file PDBOutput.hh.

Referenced by add_info(), output_info(), and remove_info().

core::Real protocols::dna::PDBOutput::mainchain_torsion_diff_threshold_

private

Definition at line 90 of file PDBOutput.hh.

Referenced by residues_are_different().

PoseOP protocols::dna::PDBOutput::pose_copy_

private

Definition at line 87 of file PDBOutput.hh.

Referenced by final_pose(), get_residue_indices_to_output(), operator()(), output_buried_unsatisfied_hbonds(), output_design_tags(), output_hbond_info(), output_pdb(), and output_score_info().

PoseCOP protocols::dna::PDBOutput::reference_pose_

private

Definition at line 88 of file PDBOutput.hh.

Referenced by get_residue_indices_to_output(), output_design_tags(), and reference_pose().

utility::vector1< core::Size > protocols::dna::PDBOutput::res_indices_to_output_

private

Definition at line 93 of file PDBOutput.hh.

Referenced by get_residue_indices_to_output(), output_buried_unsatisfied_hbonds(), output_hbond_info(), output_pdb(), and output_score_info().

ScoreFunctionOP protocols::dna::PDBOutput::score_function_

private

Definition at line 89 of file PDBOutput.hh.

Referenced by output_hbond_info(), output_pdb(), output_score_info(), and score_function().

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

src/protocols/dna/PDBOutput.hh
src/protocols/dna/PDBOutput.cc

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_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation