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Rosetta
2021.16
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Rosetta
2021.16
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#include <PDBJobOutputter.hh>
Public Types | |
| 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 | |
| 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 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... | |
Protected Member Functions | |
| 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... | |
this simplest implementation of JobOutputter outputs raw PDBs and associated files, uncompressed.
| protocols::jd2::PDBJobOutputter::PDBJobOutputter | ( | ) |
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overridedefault |
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overrideprotectedvirtual |
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)
this function outputs the final result of a job. This implementation will write a PDB file (plus scores). 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). 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. this is the master function for determining the unique output identifier for a 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 this function extracts the pose's scores for printing this function extracts the pose's scores and outputs them as a string to be packaged in an output structure.
Refactored in the 2016 Chemical XRW (eXtreme Rosetta Workshop) by Vikram K. Mulligan (vmullig@uw.edu).
| [in] | job | Const-access owning pointer to the job from which the data will be extracted. |
| [out] | data_out | A string in which the data will be stored, that can later be passed to whatever container wants it. protected PDB output///////////////////////////////////// This is the function actually different between mmCIF and PDB output, and unshared by the wwPDB parent class. Here it causes a pdb file to be written. Pure virtual in the base class. filename is an optional label for the score data table, not an actual control. |
private function (just prevents code duplication) to fill ozstream
Implements protocols::jd2::wwPDBJobOutputter.
References core::io::pdb::dump_pdb(), and protocols::jd2::wwPDBJobOutputter::extract_data_from_Job().
Referenced by protocols::enzdes::EnzdesJobOutputter::scorefile().
1.8.7