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protocols::dna::PDBOutput Class Reference

#include <PDBOutput.hh>

Inheritance diagram for protocols::dna::PDBOutput:
Inheritance graph

Public Types

typedef std::list< std::string > Strings
typedef std::map< std::string,
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::conformation::Residue Residue
typedef utility::io::ozstream ozstream
- Public Types inherited from protocols::jd2::PDBJobOutputter
- Public Types inherited from protocols::jd2::wwPDBJobOutputter
- Public Types inherited from protocols::jd2::FileJobOutputter

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::Sizeres_indices_to_output_
utility::vector1< booldesigned_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 utility::io::ozstream protocols::dna::PDBOutput::ozstream
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 ( )

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

References enabled_.

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

References enabled_.

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

JobDistributor calls this method.

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


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

functor for non-JobDistributor usage

scores pdb


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

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

outputs a set of tags describing how residues varied


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

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

Referenced by operator()().

void protocols::dna::PDBOutput::output_pdb ( ozstream pdbout)
void protocols::dna::PDBOutput::output_score_info ( ozstream pdbout)
void protocols::dna::PDBOutput::reference_pose ( Pose const &  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
void protocols::dna::PDBOutput::score_function ( ScoreFunction const &  sf)
ScoreFunctionCOP protocols::dna::PDBOutput::score_function ( ) const

References score_function_.

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

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().

Member Data Documentation

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

Referenced by residues_are_different().

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

Referenced by designed_residue(), and reference_pose().

bool protocols::dna::PDBOutput::enabled_
StringsMap protocols::dna::PDBOutput::info_map_

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

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

Referenced by residues_are_different().

PoseOP protocols::dna::PDBOutput::pose_copy_
PoseCOP protocols::dna::PDBOutput::reference_pose_
utility::vector1< core::Size > protocols::dna::PDBOutput::res_indices_to_output_
ScoreFunctionOP protocols::dna::PDBOutput::score_function_

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