pose_outputters

Bindings for protocols::jd3::pose_outputters namespace

class pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification

Bases: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification

The %PoseOutputSpecification

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification, : pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification

C++: protocols::jd3::pose_outputters::PoseOutputSpecification::operator=(const class protocols::jd3::pose_outputters::PoseOutputSpecification &) –> class protocols::jd3::pose_outputters::PoseOutputSpecification &

jd_output_suffix(*args, **kwargs)

Overloaded function.

  1. jd_output_suffix(self: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification) -> str

C++: protocols::jd3::output::OutputSpecification::jd_output_suffix() const –> const std::string &

  1. jd_output_suffix(self: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification, setting: str) -> None

C++: protocols::jd3::output::OutputSpecification::jd_output_suffix(const class std::basic_string<char> &) –> void

output_index(*args, **kwargs)

Overloaded function.

  1. output_index(self: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification) -> pyrosetta.rosetta.protocols.jd3.JobOutputIndex

C++: protocols::jd3::output::OutputSpecification::output_index() const –> struct protocols::jd3::JobOutputIndex

  1. output_index(self: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification, setting: pyrosetta.rosetta.protocols.jd3.JobOutputIndex) -> None

C++: protocols::jd3::output::OutputSpecification::output_index(const struct protocols::jd3::JobOutputIndex &) –> void

outputter_type(*args, **kwargs)

Overloaded function.

  1. outputter_type(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification) -> str

C++: protocols::jd3::pose_outputters::PoseOutputSpecification::outputter_type() const –> const std::string &

  1. outputter_type(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification, setting: str) -> None

C++: protocols::jd3::pose_outputters::PoseOutputSpecification::outputter_type(const class std::basic_string<char> &) –> void

result_id(*args, **kwargs)

Overloaded function.

  1. result_id(self: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification) -> Tuple[int, int]

C++: protocols::jd3::output::OutputSpecification::result_id() const –> struct std::pair<unsigned long, unsigned long>

  1. result_id(self: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification, setting: Tuple[int, int]) -> None

C++: protocols::jd3::output::OutputSpecification::result_id(const struct std::pair<unsigned long, unsigned long> &) –> void

suffix_from_jd_with_sep(self: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification) → str

C++: protocols::jd3::output::OutputSpecification::suffix_from_jd_with_sep() const –> std::string

class pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter

Bases: pyrosetta.rosetta.protocols.jd3.output.ResultOutputter

The %PoseOutputter

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, : pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter

C++: protocols::jd3::pose_outputters::PoseOutputter::operator=(const class protocols::jd3::pose_outputters::PoseOutputter &) –> class protocols::jd3::pose_outputters::PoseOutputter &

class_key(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter) → str

Return the stiring used to identify this class

C++: protocols::jd3::pose_outputters::PoseOutputter::class_key() const –> std::string

create_output_specification(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, job: protocols::jd3::LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, outputter_tag: pyrosetta.rosetta.utility.tag.Tag) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification

Create the PoseOutputSpecification for a particular job

C++: protocols::jd3::pose_outputters::PoseOutputter::create_output_specification(const class protocols::jd3::LarvalJob &, const struct protocols::jd3::JobOutputIndex &, const class utility::options::OptionCollection &, class std::shared_ptr<const class utility::tag::Tag>) –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputSpecification>

determine_job_tag(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → None

Determine the inner-larval job’s “job_tag” from the <Output> tag / per-job options

C++: protocols::jd3::pose_outputters::PoseOutputter::determine_job_tag(class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &, class protocols::jd3::InnerLarvalJob &) const –> void

flush(self: pyrosetta.rosetta.protocols.jd3.output.ResultOutputter) → None
Output from an outputter may be held back and only flushed when requested
by the JobQueen; I/O can be expensive, so it’s a good idea to gather up the results of many outputs before flushing them to disk.

C++: protocols::jd3::output::ResultOutputter::flush() –> void

job_has_already_completed(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, job: protocols::jd3::LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection) → bool

C++: protocols::jd3::pose_outputters::PoseOutputter::job_has_already_completed(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &) const –> bool

mark_job_as_having_started(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, job: protocols::jd3::LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection) → None

C++: protocols::jd3::pose_outputters::PoseOutputter::mark_job_as_having_started(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &) const –> void

outputter_for_job(*args, **kwargs)

Overloaded function.

  1. outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, outputter_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str
Return an identifier string for the specific instance of the %PoseOutputter that ought to be used
for a particular job so that the %PoseOutputter can e.g. aggregate all of the outputs for a group of jobs and output them all at once when flush is called. The outputter may return the empty string if all outputters (of the same type) are interchangable (e.g. the PDBPoseOutputter). e.g., the SilentFilePoseOutputter returns the name of the file that it sends its outputs to.

C++: protocols::jd3::pose_outputters::PoseOutputter::outputter_for_job(class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &, const class protocols::jd3::InnerLarvalJob &) const –> std::string

  1. outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, spec: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification) -> str
Return an identifier string for the specific instance of the %PoseOutputter that ought to be used
for a particular job so that the %PoseOutputter can e.g. aggregate all of the outputs for a group of jobs and output them all at once when flush is called. The outputter may return the empty string if all outputters (of the same type) are interchangable (e.g. the PDBPoseOutputter). e.g., the SilentFilePoseOutputter returns the name of the file that it sends its outputs to. This function respects the output-filename-suffix that may have been provided by the JobDistributor

C++: protocols::jd3::pose_outputters::PoseOutputter::outputter_for_job(const class protocols::jd3::pose_outputters::PoseOutputSpecification &) const –> std::string

write_output(self: pyrosetta.rosetta.protocols.jd3.output.ResultOutputter, specification: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification, result: protocols::jd3::JobResult) → None

C++: protocols::jd3::output::ResultOutputter::write_output(const class protocols::jd3::output::OutputSpecification &, const class protocols::jd3::JobResult &) –> void

class pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter

Bases: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter

The %SecondaryPoseOutputter

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter, : pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter) → pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter

C++: protocols::jd3::pose_outputters::SecondaryPoseOutputter::operator=(const class protocols::jd3::pose_outputters::SecondaryPoseOutputter &) –> class protocols::jd3::pose_outputters::SecondaryPoseOutputter &

class_key(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter) → str

Return the stiring used to identify this class

C++: protocols::jd3::pose_outputters::PoseOutputter::class_key() const –> std::string

create_output_specification(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, job: protocols::jd3::LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, outputter_tag: pyrosetta.rosetta.utility.tag.Tag) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification

Create the PoseOutputSpecification for a particular job

C++: protocols::jd3::pose_outputters::PoseOutputter::create_output_specification(const class protocols::jd3::LarvalJob &, const struct protocols::jd3::JobOutputIndex &, const class utility::options::OptionCollection &, class std::shared_ptr<const class utility::tag::Tag>) –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputSpecification>

determine_job_tag(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → None
This responsibility does not belong in the SecondaryPoseOutputter, so it receives
a no-op implementation in the base class – it is primarily the responsibility of the PoseOutputter base class and will not / should not be asked of the SecondaryPoseOutputter.

C++: protocols::jd3::pose_outputters::SecondaryPoseOutputter::determine_job_tag(class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &, class protocols::jd3::InnerLarvalJob &) const –> void

flush(self: pyrosetta.rosetta.protocols.jd3.output.ResultOutputter) → None
Output from an outputter may be held back and only flushed when requested
by the JobQueen; I/O can be expensive, so it’s a good idea to gather up the results of many outputs before flushing them to disk.

C++: protocols::jd3::output::ResultOutputter::flush() –> void

job_has_already_completed(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter, job: protocols::jd3::LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection) → bool
This responsibility does not belong in the SecondaryPoseOutputter, so it receives
a no-frills implementation in the base class – it is primarily the responsibility of the PoseOutputter base class and will not / should not be asked of the SecondaryPoseOutputter.

C++: protocols::jd3::pose_outputters::SecondaryPoseOutputter::job_has_already_completed(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &) const –> bool

mark_job_as_having_started(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter, job: protocols::jd3::LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection) → None
This responsibility does not belong in the SecondaryPoseOutputter, so it receives
a no-op implementation in the base class – it is primarily the responsibility of the PoseOutputter base class and will not / should not be asked of the SecondaryPoseOutputter.

C++: protocols::jd3::pose_outputters::SecondaryPoseOutputter::mark_job_as_having_started(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &) const –> void

outputter_for_job(*args, **kwargs)

Overloaded function.

  1. outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, outputter_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str
Return an identifier string for the specific instance of the %PoseOutputter that ought to be used
for a particular job so that the %PoseOutputter can e.g. aggregate all of the outputs for a group of jobs and output them all at once when flush is called. The outputter may return the empty string if all outputters (of the same type) are interchangable (e.g. the PDBPoseOutputter). e.g., the SilentFilePoseOutputter returns the name of the file that it sends its outputs to.

C++: protocols::jd3::pose_outputters::PoseOutputter::outputter_for_job(class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &, const class protocols::jd3::InnerLarvalJob &) const –> std::string

  1. outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, spec: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification) -> str
Return an identifier string for the specific instance of the %PoseOutputter that ought to be used
for a particular job so that the %PoseOutputter can e.g. aggregate all of the outputs for a group of jobs and output them all at once when flush is called. The outputter may return the empty string if all outputters (of the same type) are interchangable (e.g. the PDBPoseOutputter). e.g., the SilentFilePoseOutputter returns the name of the file that it sends its outputs to. This function respects the output-filename-suffix that may have been provided by the JobDistributor

C++: protocols::jd3::pose_outputters::PoseOutputter::outputter_for_job(const class protocols::jd3::pose_outputters::PoseOutputSpecification &) const –> std::string

write_output(self: pyrosetta.rosetta.protocols.jd3.output.ResultOutputter, specification: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification, result: protocols::jd3::JobResult) → None

C++: protocols::jd3::output::ResultOutputter::write_output(const class protocols::jd3::output::OutputSpecification &, const class protocols::jd3::JobResult &) –> void