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protocols::jd2::AtomTreeDiffJobOutputter Class Reference

#include <AtomTreeDiffJobOutputter.hh>

Inheritance diagram for protocols::jd2::AtomTreeDiffJobOutputter:
Inheritance graph
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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 ( )
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
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 
)
overridevirtual

this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::call_output_observers().

std::string protocols::jd2::AtomTreeDiffJobOutputter::output_name ( JobCOP  job)
overridevirtual

this is the master function for determining the unique output identifier for a job

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::affixed_numbered_name().

Referenced by final_pose(), and job_has_completed().

void protocols::jd2::AtomTreeDiffJobOutputter::set_precision ( int  bb_precision,
int  sc_precision,
int  bondlen_precision 
)

what precision should the atom_tree_diff be ouput at?

References bb_precision_, bondlen_precision_, and sc_precision_.

Referenced by AtomTreeDiffJobOutputter().

void protocols::jd2::AtomTreeDiffJobOutputter::use_input_for_ref ( bool  use_input = true)

use input as reference pose?

References last_ref_tag_, and use_input_.

Member Data Documentation

core::import_pose::atom_tree_diffs::AtomTreeDiff protocols::jd2::AtomTreeDiffJobOutputter::atom_tree_diff_
private
int protocols::jd2::AtomTreeDiffJobOutputter::bb_precision_
private

precision to output atom tree diff at.

Referenced by dump_pose(), and set_precision().

int protocols::jd2::AtomTreeDiffJobOutputter::bondlen_precision_
private

Referenced by dump_pose(), and set_precision().

core::pose::Pose protocols::jd2::AtomTreeDiffJobOutputter::last_ref_pose_
private

Referenced by dump_pose().

std::string protocols::jd2::AtomTreeDiffJobOutputter::last_ref_tag_
private

Referenced by dump_pose(), and use_input_for_ref().

utility::io::ozstream protocols::jd2::AtomTreeDiffJobOutputter::out_
private

Referenced by dump_pose().

std::string protocols::jd2::AtomTreeDiffJobOutputter::outfile_name_
private
int protocols::jd2::AtomTreeDiffJobOutputter::sc_precision_
private

Referenced by dump_pose(), and set_precision().

bool protocols::jd2::AtomTreeDiffJobOutputter::use_input_
private

use input as reference pose? (default false)

Referenced by dump_pose(), and use_input_for_ref().

std::set< std::string > protocols::jd2::AtomTreeDiffJobOutputter::used_tags_
private

Referenced by dump_pose(), and job_has_completed().


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