pose_outputters¶

Bindings for protocols::jd3::pose_outputters namespace

class pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter¶

Bases: PoseOutputter

The %DeNovoSilentFilePoseOutputter

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter, : pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter) → pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::operator=(const class protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter &) –> class protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter &

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

Return the string used by the DeNovoSilentFilePoseOutputterCreator to identify the: class in an XML file (which is the string returned by the static keyname method)

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

create_output_specification(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, job_options: pyrosetta.rosetta.utility.options.OptionCollection, tag: pyrosetta.rosetta.utility.tag.Tag) → protocols::jd3::pose_outputters::PoseOutputSpecification¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::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.DeNovoSilentFilePoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → None¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::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.pose_outputters.DeNovoSilentFilePoseOutputter) → None¶

Write out all cached silent files – may happen after an exception is caught by: the JobDistributor and the process is about to be spun down.

C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::flush() –> void

job_has_already_completed(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection) → bool¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::job_has_already_completed(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &) const –> bool

static keyname() → str¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::keyname() –> std::string

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

outputter_for_job(*args, **kwargs)¶

Overloaded function.

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str

C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::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

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter, spec: protocols::jd3::pose_outputters::PoseOutputSpecification) -> str

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

static outputter_specified_by_command_line() → bool¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::outputter_specified_by_command_line() –> bool

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

write_output(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter, spec: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification, result: pyrosetta.rosetta.protocols.jd3.JobResult) → None¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::write_output(const class protocols::jd3::output::OutputSpecification &, const class protocols::jd3::JobResult &) –> void

class pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator¶

Bases: PoseOutputterCreator

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator::operator=(const class protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator &) –> class protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator &

create_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator::create_outputter() const –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator) → str¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

outputter_specified_by_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator) → bool¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator::outputter_specified_by_command_line() const –> bool

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification¶

Bases: PoseOutputSpecification

The %PDBPoseOutputSpecification giving all of the details of how to write a Pose out to disk in PDB format.

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification, : pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputSpecification::operator=(const class protocols::jd3::pose_outputters::PDBPoseOutputSpecification &) –> class protocols::jd3::pose_outputters::PDBPoseOutputSpecification &

jd_output_suffix(*args, **kwargs)¶

Overloaded function.

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

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

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

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

out_fname(*args, **kwargs)¶

Overloaded function.

out_fname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification) -> str

C++: protocols::jd3::pose_outputters::PDBPoseOutputSpecification::out_fname() const –> std::string

out_fname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification, setting: str) -> None

C++: protocols::jd3::pose_outputters::PDBPoseOutputSpecification::out_fname(const std::string &) –> void

output_index(*args, **kwargs)¶

Overloaded function.

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

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.

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

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

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

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

result_id(*args, **kwargs)¶

Overloaded function.

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>

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

sfr_opts(*args, **kwargs)¶

Overloaded function.

sfr_opts(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification) -> pyrosetta.rosetta.core.io.StructFileRepOptions

C++: protocols::jd3::pose_outputters::PDBPoseOutputSpecification::sfr_opts() const –> class std::shared_ptr<const class core::io::StructFileRepOptions>

sfr_opts(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification, setting: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

C++: protocols::jd3::pose_outputters::PDBPoseOutputSpecification::sfr_opts(const class core::io::StructFileRepOptions &) –> 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.PDBPoseOutputter¶

Bases: PoseOutputter

The %PDBPoseOutputter

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, : pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::operator=(const class protocols::jd3::pose_outputters::PDBPoseOutputter &) –> class protocols::jd3::pose_outputters::PDBPoseOutputter &

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

Return the stiring used by the PDBPoseOutputterCreator for this class

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

create_output_specification(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, 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::PDBPoseOutputter::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.PDBPoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → None¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::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.pose_outputters.PDBPoseOutputter) → None¶

Currently a no-op since the “write output pose” method sends all: outputs to disk.

C++: protocols::jd3::pose_outputters::PDBPoseOutputter::flush() –> void

job_has_already_completed(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection) → bool¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::job_has_already_completed(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &) const –> bool

static keyname() → str¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::keyname() –> std::string

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

output_name(*args, **kwargs)¶

Overloaded function.

output_name(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection, tag: pyrosetta.rosetta.utility.tag.Tag) -> str

Guess on the name of the output PDB using just the LarvalJob – i.e. in the absence of

the JobOutputIndex

Public for testing

C++: protocols::jd3::pose_outputters::PDBPoseOutputter::output_name(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &, class std::shared_ptr<const class utility::tag::Tag>) const –> std::string

output_name(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, tag: pyrosetta.rosetta.utility.tag.Tag) -> str

Public for testing

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

outputter_for_job(*args, **kwargs)¶

Overloaded function.

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str

C++: protocols::jd3::pose_outputters::PDBPoseOutputter::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

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, spec: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification) -> str

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

static outputter_specified_by_command_line() → bool¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::outputter_specified_by_command_line() –> bool

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

Write a pose out to permanent storage (whatever that may be).

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

class pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator¶

Bases: PoseOutputterCreator

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputterCreator::operator=(const class protocols::jd3::pose_outputters::PDBPoseOutputterCreator &) –> class protocols::jd3::pose_outputters::PDBPoseOutputterCreator &

create_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputterCreator::create_outputter() const –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator) → str¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

outputter_specified_by_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator) → bool¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputterCreator::outputter_specified_by_command_line() const –> bool

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

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

Bases: 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.

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

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

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

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

output_index(*args, **kwargs)¶

Overloaded function.

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

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.

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

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

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

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

result_id(*args, **kwargs)¶

Overloaded function.

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>

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: 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: pyrosetta.rosetta.protocols.jd3.LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, outputter_tag: pyrosetta.rosetta.utility.tag.Tag) → 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: pyrosetta.rosetta.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

outputter_for_job(*args, **kwargs)¶

Overloaded function.

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

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, spec: 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: pyrosetta.rosetta.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.PoseOutputterCreator¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator¶: C++: protocols::jd3::pose_outputters::PoseOutputterCreator::operator=(const class protocols::jd3::pose_outputters::PoseOutputterCreator &) –> class protocols::jd3::pose_outputters::PoseOutputterCreator &

create_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter¶: C++: protocols::jd3::pose_outputters::PoseOutputterCreator::create_outputter() const –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator) → str¶: C++: protocols::jd3::pose_outputters::PoseOutputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::PoseOutputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

outputter_specified_by_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator) → bool¶: C++: protocols::jd3::pose_outputters::PoseOutputterCreator::outputter_specified_by_command_line() const –> bool

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::PoseOutputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory¶

Bases: SingletonBase_protocols_jd3_pose_outputters_PoseOutputterFactory_t

static complex_type_name_for_pose_outputter(outputter_key: str) → str¶: C++: protocols::jd3::pose_outputters::PoseOutputterFactory::complex_type_name_for_pose_outputter(const std::string &) –> std::string

static complex_type_name_for_secondary_pose_outputter(outputter_key: str) → str¶: C++: protocols::jd3::pose_outputters::PoseOutputterFactory::complex_type_name_for_secondary_pose_outputter(const std::string &) –> std::string

define_pose_outputter_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory, xsd: utility::tag::XMLSchemaDefinition) → None¶

The %PoseOutputterFactory is the point of entry for the definition of the XML Schemas: for every PoseOutputter that may be instantiated from a file. It is responsible for defining an xs:group named “pose_outputter” listing each of the pose-outputter-complex types that may be initialized using the %PoseOutputterFactory and to iterate across each of the PoseOutputterCreators it contains asking them for the XML schema of the PoseOutputter they are responsible for creating.

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::define_pose_outputter_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

define_secondary_pose_outputter_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory, xsd: utility::tag::XMLSchemaDefinition) → None¶

The %PoseOutputterFactory is the point of entry for the definition of the XML Schemas: for every SecondaryPoseOutputter that may be instantiated from a file. It is responsible for defining an xs:group named “secondary_pose_outputter” listing each of the pose-outputter-complex types that may be initialized using the %PoseOutputterFactory and to iterate across each of the SecondaryPoseOutputterCreators it contains asking them for the XML schema of the SecondaryPoseOutputter they are responsible for creating.

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::define_secondary_pose_outputter_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(*args, **kwargs)¶

Overloaded function.

factory_register(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory, creator: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator) -> None

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::factory_register(class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputterCreator>) –> void

factory_register(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory, creator: protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator) -> None

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::factory_register(class std::shared_ptr<class protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator>) –> void

static get_instance() → protocols::jd3::pose_outputters::PoseOutputterFactory¶: C++: utility::SingletonBase<protocols::jd3::pose_outputters::PoseOutputterFactory>::get_instance() –> class protocols::jd3::pose_outputters::PoseOutputterFactory *

list_outputter_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::PoseOutputterFactory::list_outputter_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

list_secondary_outputter_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::PoseOutputterFactory::list_secondary_outputter_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

new_pose_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory, : str) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter¶

Create a pose outputter given its identifying string, e.g. the name of an XML element.

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::new_pose_outputter(const std::string &) const –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputter>

new_secondary_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory, : str) → protocols::jd3::pose_outputters::SecondaryPoseOutputter¶

Create a SecondaryPoseOutputter given its identifying string, e.g. the name of an XML element.

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::new_secondary_outputter(const std::string &) const –> class std::shared_ptr<class protocols::jd3::pose_outputters::SecondaryPoseOutputter>

pose_outputter_creators(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory) → pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t¶: C++: protocols::jd3::pose_outputters::PoseOutputterFactory::pose_outputter_creators() const –> const class std::list<class std::shared_ptr<const class protocols::jd3::pose_outputters::PoseOutputterCreator>, class std::allocator<class std::shared_ptr<const class protocols::jd3::pose_outputters::PoseOutputterCreator> > > &

pose_outputter_from_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter¶

Construct a PoseOutputter for a job relying on the command line in the absence of a specified: outputter class in the job-definition file.

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::pose_outputter_from_command_line() const –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputter>

static pose_outputter_xml_schema_group_name() → str¶: C++: protocols::jd3::pose_outputters::PoseOutputterFactory::pose_outputter_xml_schema_group_name() –> std::string

secondary_pose_outputter_creators(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory) → pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t¶: C++: protocols::jd3::pose_outputters::PoseOutputterFactory::secondary_pose_outputter_creators() const –> const class std::list<class std::shared_ptr<const class protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator>, class std::allocator<class std::shared_ptr<const class protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator> > > &

static secondary_pose_outputter_xml_schema_group_name() → str¶: C++: protocols::jd3::pose_outputters::PoseOutputterFactory::secondary_pose_outputter_xml_schema_group_name() –> std::string

secondary_pose_outputters_from_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t¶

Construct all SecondaryPoseOutputters for a job relying on the command line in the absence of a specified: list of outputter classes in the job-definition file.

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::secondary_pose_outputters_from_command_line() const –> class std::list<class std::shared_ptr<class protocols::jd3::pose_outputters::SecondaryPoseOutputter>, class std::allocator<class std::shared_ptr<class protocols::jd3::pose_outputters::SecondaryPoseOutputter> > >

set_throw_on_double_registration(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory) → None¶

Should the Factory throw an exception or call utility::exit when it encounters the: second of two PoseOutputterCreators or two SecondaryPoseOutputters with the same keyname? It’s default behavior is to call utility::exit, but this method allows you to set it so that it will throw an exception instead (which is unit testable).

C++: protocols::jd3::pose_outputters::PoseOutputterFactory::set_throw_on_double_registration() –> void

class pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification¶

Bases: PoseOutputSpecification

The %ScoreFileOutputSpecification giving all of the details of how to write a Pose out to disk in PDB format.

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification, : pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification) → pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputSpecification::operator=(const class protocols::jd3::pose_outputters::ScoreFileOutputSpecification &) –> class protocols::jd3::pose_outputters::ScoreFileOutputSpecification &

jd_output_suffix(*args, **kwargs)¶

Overloaded function.

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

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

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

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

out_fname(*args, **kwargs)¶

Overloaded function.

out_fname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification) -> str

C++: protocols::jd3::pose_outputters::ScoreFileOutputSpecification::out_fname() const –> std::string

out_fname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification, setting: str) -> None

C++: protocols::jd3::pose_outputters::ScoreFileOutputSpecification::out_fname(const std::string &) –> void

output_index(*args, **kwargs)¶

Overloaded function.

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

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.

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

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

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

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

pose_tag(*args, **kwargs)¶

Overloaded function.

pose_tag(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification) -> str

C++: protocols::jd3::pose_outputters::ScoreFileOutputSpecification::pose_tag() const –> const std::string &

pose_tag(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification, setting: str) -> None

C++: protocols::jd3::pose_outputters::ScoreFileOutputSpecification::pose_tag(const std::string &) –> void

result_id(*args, **kwargs)¶

Overloaded function.

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>

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.ScoreFileOutputter¶

Bases: SecondaryPoseOutputter

The %ScoreFileOutputter

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter, : pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter) → pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputter::operator=(const class protocols::jd3::pose_outputters::ScoreFileOutputter &) –> class protocols::jd3::pose_outputters::ScoreFileOutputter &

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

Return the stiring used by the ScoreFileOutputterCreator for this class

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

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

Using the LarvalJob’s job_tag (determined by the (primary) JobOutputter),: write extra data about this output Pose to its destination.

C++: protocols::jd3::pose_outputters::ScoreFileOutputter::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

filename_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, : pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → pyrosetta.rosetta.utility.file.FileName¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputter::filename_for_job(class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &, const class protocols::jd3::InnerLarvalJob &) const –> class utility::file::FileName

flush(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter) → None¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputter::flush() –> void

job_has_already_completed(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter, job: pyrosetta.rosetta.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

static keyname() → str¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputter::keyname() –> std::string

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputter::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

outputter_for_job(*args, **kwargs)¶

Overloaded function.

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str

The %ScoreFileOutputter returns the name of the scorefile that it sends its outputs to: for this particular job so that the JobQueen can send multiple outputs to the same outputter before invoking flush()

C++: protocols::jd3::pose_outputters::ScoreFileOutputter::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

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter, spec: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification) -> str

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

static outputter_specified_by_command_line() → bool¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputter::outputter_specified_by_command_line() –> bool

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

Write out the scores for a particular Pose (held in the JobResult) to a score file

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

class pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator¶

Bases: SecondaryPoseOutputterCreator

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputterCreator::operator=(const class protocols::jd3::pose_outputters::ScoreFileOutputterCreator &) –> class protocols::jd3::pose_outputters::ScoreFileOutputterCreator &

create_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputterCreator::create_outputter() const –> class std::shared_ptr<class protocols::jd3::pose_outputters::SecondaryPoseOutputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator) → str¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

outputter_specified_by_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator) → bool¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputterCreator::outputter_specified_by_command_line() const –> bool

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::ScoreFileOutputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

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

Bases: 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: pyrosetta.rosetta.protocols.jd3.LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, outputter_tag: pyrosetta.rosetta.utility.tag.Tag) → 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: pyrosetta.rosetta.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

outputter_for_job(*args, **kwargs)¶

Overloaded function.

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

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter, spec: 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: pyrosetta.rosetta.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.SecondaryPoseOutputterCreator¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator¶: C++: protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator::operator=(const class protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator &) –> class protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator &

create_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter¶: C++: protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator::create_outputter() const –> class std::shared_ptr<class protocols::jd3::pose_outputters::SecondaryPoseOutputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator) → str¶: C++: protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

outputter_specified_by_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator) → bool¶: C++: protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator::outputter_specified_by_command_line() const –> bool

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification¶

Bases: PoseOutputSpecification

The %SilentFilePoseOutputSpecification giving all of the details of how to write a Pose out to disk as a silent file

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification, : pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification) → pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::operator=(const class protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification &) –> class protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification &

buffer_limit(*args, **kwargs)¶

Overloaded function.

buffer_limit(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification) -> int

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::buffer_limit() const –> unsigned long

buffer_limit(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification, setting: int) -> None

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::buffer_limit(unsigned long) –> void

jd_output_suffix(*args, **kwargs)¶

Overloaded function.

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

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

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

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

out_fname(*args, **kwargs)¶

Overloaded function.

out_fname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification) -> str

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::out_fname() const –> std::string

out_fname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification, setting: str) -> None

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::out_fname(const std::string &) –> void

output_index(*args, **kwargs)¶

Overloaded function.

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

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.

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

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

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

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

pose_tag(*args, **kwargs)¶

Overloaded function.

pose_tag(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification) -> str

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::pose_tag() const –> const std::string &

pose_tag(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification, setting: str) -> None

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::pose_tag(const std::string &) –> void

result_id(*args, **kwargs)¶

Overloaded function.

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>

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

sf_opts(*args, **kwargs)¶

Overloaded function.

sf_opts(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification) -> pyrosetta.rosetta.core.io.silent.SilentFileOptions

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::sf_opts() const –> const class core::io::silent::SilentFileOptions &

sf_opts(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification, setting: pyrosetta.rosetta.core.io.silent.SilentFileOptions) -> None

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification::sf_opts(const class core::io::silent::SilentFileOptions &) –> 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.SilentFilePoseOutputter¶

Bases: PoseOutputter

The %SilentFilePoseOutputter

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter, : pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter) → pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::operator=(const class protocols::jd3::pose_outputters::SilentFilePoseOutputter &) –> class protocols::jd3::pose_outputters::SilentFilePoseOutputter &

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

Return the string used by the SilentFilePoseOutputterCreator to identify the: class in an XML file (which is the string returned by the static keyname method)

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

create_output_specification(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, 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::SilentFilePoseOutputter::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.SilentFilePoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → None¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::determine_job_tag(class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &, class protocols::jd3::InnerLarvalJob &) const –> void

filename_for_output_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter, outputter_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection) → str¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::filename_for_output_job(class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &) const –> std::string

flush(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter) → None¶

Write out all cached silent files – may happen after an exception is caught by: the JobDistributor and the process is about to be spun down.

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::flush() –> void

job_has_already_completed(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection) → bool¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::job_has_already_completed(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &) const –> bool

static keyname() → str¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::keyname() –> std::string

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

outputter_for_job(*args, **kwargs)¶

Overloaded function.

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str

C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::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

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter, spec: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification) -> str

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

static outputter_specified_by_command_line() → bool¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::outputter_specified_by_command_line() –> bool

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

write_output(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter, spec: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification, result: pyrosetta.rosetta.protocols.jd3.JobResult) → None¶

Write a pose out to permanent storage (whatever that may be).

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

class pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator¶

Bases: PoseOutputterCreator

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator::operator=(const class protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator &) –> class protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator &

create_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator::create_outputter() const –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator) → str¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

outputter_specified_by_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator) → bool¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator::outputter_specified_by_command_line() const –> bool

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification¶

Bases: PoseOutputSpecification

The %mmTFPoseOutputSpecification giving all of the details of how to write a Pose out to disk in PDB format.

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification, : pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification) → pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputSpecification::operator=(const class protocols::jd3::pose_outputters::mmTFPoseOutputSpecification &) –> class protocols::jd3::pose_outputters::mmTFPoseOutputSpecification &

jd_output_suffix(*args, **kwargs)¶

Overloaded function.

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

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

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

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

out_fname(*args, **kwargs)¶

Overloaded function.

out_fname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification) -> str

C++: protocols::jd3::pose_outputters::mmTFPoseOutputSpecification::out_fname() const –> std::string

out_fname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification, setting: str) -> None

C++: protocols::jd3::pose_outputters::mmTFPoseOutputSpecification::out_fname(const std::string &) –> void

output_index(*args, **kwargs)¶

Overloaded function.

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

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.

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

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

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

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

result_id(*args, **kwargs)¶

Overloaded function.

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>

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

sfr_opts(*args, **kwargs)¶

Overloaded function.

sfr_opts(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification) -> pyrosetta.rosetta.core.io.StructFileRepOptions

C++: protocols::jd3::pose_outputters::mmTFPoseOutputSpecification::sfr_opts() const –> class std::shared_ptr<const class core::io::StructFileRepOptions>

sfr_opts(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification, setting: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

C++: protocols::jd3::pose_outputters::mmTFPoseOutputSpecification::sfr_opts(const class core::io::StructFileRepOptions &) –> 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.mmTFPoseOutputter¶

Bases: PDBPoseOutputter

The %mmTFPoseOutputter

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter, : pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter) → pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputter::operator=(const class protocols::jd3::pose_outputters::mmTFPoseOutputter &) –> class protocols::jd3::pose_outputters::mmTFPoseOutputter &

class_key(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter) → str¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputter::class_key() const –> std::string

create_output_specification(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, 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::mmTFPoseOutputter::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.PDBPoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → None¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::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.pose_outputters.PDBPoseOutputter) → None¶

Currently a no-op since the “write output pose” method sends all: outputs to disk.

C++: protocols::jd3::pose_outputters::PDBPoseOutputter::flush() –> void

job_has_already_completed(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, options: pyrosetta.rosetta.utility.options.OptionCollection) → bool¶: C++: protocols::jd3::pose_outputters::PDBPoseOutputter::job_has_already_completed(const class protocols::jd3::LarvalJob &, const class utility::options::OptionCollection &) const –> bool

static keyname() → str¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputter::keyname() –> std::string

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputter::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

output_name(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, output_index: pyrosetta.rosetta.protocols.jd3.JobOutputIndex, options: pyrosetta.rosetta.utility.options.OptionCollection, tag: pyrosetta.rosetta.utility.tag.Tag) → str¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputter::output_name(const class protocols::jd3::LarvalJob &, const struct protocols::jd3::JobOutputIndex &, const class utility::options::OptionCollection &, class std::shared_ptr<const class utility::tag::Tag>) const –> std::string

outputter_for_job(*args, **kwargs)¶

Overloaded function.

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, output_tag: pyrosetta.rosetta.utility.tag.Tag, job_options: pyrosetta.rosetta.utility.options.OptionCollection, job: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str

C++: protocols::jd3::pose_outputters::PDBPoseOutputter::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

outputter_for_job(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter, spec: pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification) -> str

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

static outputter_specified_by_command_line() → bool¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputter::outputter_specified_by_command_line() –> bool

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

Write a pose out to permanent storage (whatever that may be).

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

class pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator¶

Bases: PoseOutputterCreator

assign(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator, : pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputterCreator::operator=(const class protocols::jd3::pose_outputters::mmTFPoseOutputterCreator &) –> class protocols::jd3::pose_outputters::mmTFPoseOutputterCreator &

create_outputter(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator) → pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputterCreator::create_outputter() const –> class std::shared_ptr<class protocols::jd3::pose_outputters::PoseOutputter>

keyname(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator) → str¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputterCreator::keyname() const –> std::string

list_options_read(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator, read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputterCreator::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) const –> void

outputter_specified_by_command_line(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator) → bool¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputterCreator::outputter_specified_by_command_line() const –> bool

provide_xml_schema(self: pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::jd3::pose_outputters::mmTFPoseOutputterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.jd3.pose_outputters.pose_outputter_xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, outputter_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶

Define the XML schema definition for a PoseOutputter that contains: no subtags but may contain any number of attributes (aka options).

C++: protocols::jd3::pose_outputters::pose_outputter_xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void