Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
protocols::jd2::PDBJobOutputter Class Reference

#include <PDBJobOutputter.hh>

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List of all members.

Public Types

typedef
protocols::jd2::FileJobOutputter 
parent

Public Member Functions

 PDBJobOutputter ()
virtual ~PDBJobOutputter ()
virtual void final_pose (JobCOP job, core::pose::Pose const &pose)
 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)
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).
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.
virtual std::string output_name (JobCOP job)
 this is the master function for determining the unique output identifier for a job

Protected Member Functions

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
virtual void extract_scores (core::pose::Pose const &pose, utility::io::ozstream &out)
 this function extracts the pose's scores for printing
virtual void extract_data_from_Job (JobCOP job, utility::io::ozstream &out)
 this function extracts the pose's scores for printing
virtual void dump_pose (JobCOP job, core::pose::Pose const &pose, utility::io::ozstream &out)
 handles ozstream output; shared by both pdb output functions

Detailed Description

this simplest implementation of JobOutputter outputs raw PDBs and associated files, uncompressed.


Member Typedef Documentation


Constructor & Destructor Documentation

protocols::jd2::PDBJobOutputter::PDBJobOutputter ( )
protocols::jd2::PDBJobOutputter::~PDBJobOutputter ( ) [virtual]

Member Function Documentation

void protocols::jd2::PDBJobOutputter::dump_pose ( JobCOP  job,
core::pose::Pose const &  pose,
utility::io::ozstream &  out 
) [protected, virtual]

handles ozstream output; shared by both pdb output functions

protected PDB output/////////////////////////////////////

private function (just prevents code duplication) to fill ozstream

References core::io::pdb::dump_pdb(), extract_data_from_Job(), and extract_scores().

Referenced by final_pose(), other_pose(), and protocols::enzdes::EnzdesJobOutputter::scorefile().

std::string protocols::jd2::PDBJobOutputter::extended_name ( JobCOP  job) [protected, virtual]

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

References output_name().

Referenced by final_pose(), protocols::dna::PDBOutput::final_pose(), job_has_completed(), and other_pose().

void protocols::jd2::PDBJobOutputter::extract_data_from_Job ( JobCOP  job,
utility::io::ozstream &  out 
) [protected, virtual]

this function extracts the pose's scores for printing

References core::sequence::end.

Referenced by dump_pose(), and protocols::dna::PDBOutput::final_pose().

void protocols::jd2::PDBJobOutputter::extract_scores ( core::pose::Pose const &  pose,
utility::io::ozstream &  out 
) [protected, virtual]

this function extracts the pose's scores for printing

In order for this to work as expected, the Pose's cached energies must match up with the (current) conformation. A good time to do this is at the end of your protocol's apply() method: scorefxn( pose );

Referenced by dump_pose().

void protocols::jd2::PDBJobOutputter::final_pose ( JobCOP  job,
core::pose::Pose const &  pose 
) [virtual]

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).

Implements protocols::jd2::FileJobOutputter.

Reimplemented in protocols::dna::PDBOutput, and protocols::enzdes::EnzdesJobOutputter.

References dump_pose(), extended_name(), protocols::jd2::FileJobOutputter::scorefile(), and protocols::jd2::TR().

Referenced by protocols::enzdes::EnzdesJobOutputter::final_pose().

bool protocols::jd2::PDBJobOutputter::job_has_completed ( JobCOP  job) [virtual]

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.

Reimplemented in protocols::enzdes::EnzdesJobOutputter.

References extended_name(), and protocols::swa::rna::file_exists().

Referenced by protocols::enzdes::EnzdesJobOutputter::job_has_completed().

void protocols::jd2::PDBJobOutputter::other_pose ( JobCOP  job,
core::pose::Pose const &  pose,
std::string const &  tag,
int  copy_count = -1,
bool  score_only = false 
) [virtual]

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).

Implements protocols::jd2::FileJobOutputter.

References dump_pose(), extended_name(), protocols::jd2::FileJobOutputter::file(), protocols::jd2::FileJobOutputter::scorefile(), and protocols::jd2::TR().

std::string protocols::jd2::PDBJobOutputter::output_name ( JobCOP  job) [virtual]

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 extended_name(), and protocols::enzdes::EnzdesJobOutputter::scorefile().


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