standard

Bindings for protocols::jd3::standard namespace

class pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen

Bases: pyrosetta.rosetta.protocols.jd3.JobQueen

The %StandardJobQueen is meant to handle the most common form of Rosetta jobs where a protocol is applied to a single input structure to generate a single output structure. Most JobQueens in Rosetta will to derive from this JobQueen. To make the process of deriving new JobQueens easy, this class’s API has been carefully designed to be easy to work with and the class itself has been designed to do as much heavy lifting as possible and to leave only the responsibilities that the %StandardJobQueen could not perform to the derived classes.

assign(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, : pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen

C++: protocols::jd3::standard::StandardJobQueen::operator=(const class protocols::jd3::standard::StandardJobQueen &) –> class protocols::jd3::standard::StandardJobQueen &

completed_job_summary(*args, **kwargs)

Overloaded function.

1. completed_job_summary(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job: protocols::jd3::LarvalJob, result_index: int, summary: protocols::jd3::JobSummary) -> None

If the job result that is summarized here should be output, then the SJQ needs to

have access to the LarvalJob in order to do that.

C++: protocols::jd3::standard::StandardJobQueen::completed_job_summary(class std::shared_ptr<const class protocols::jd3::LarvalJob>, unsigned long, class std::shared_ptr<class protocols::jd3::JobSummary>) –> void

2. completed_job_summary(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job_id: int, result_index: int, summary: protocols::jd3::JobSummary) -> None

This method should not be called, as the SJQ needs the LarvalJob pointer when creating

OutputSpecifications.

C++: protocols::jd3::standard::StandardJobQueen::completed_job_summary(unsigned long, unsigned long, class std::shared_ptr<class protocols::jd3::JobSummary>) –> void

determine_preliminary_job_list_from_xml_file(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job_def_string: str) → None

Read from an input string representing the contents of the job-definiton XML file

and construct a set of LarvalJobs; this function is primarily useful for testing, but could be used to organize jobs by an enterprising job distributor or by another JobQueen.

C++: protocols::jd3::standard::StandardJobQueen::determine_preliminary_job_list_from_xml_file(const class std::basic_string<char> &) –> void

flush(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → None

C++: protocols::jd3::standard::StandardJobQueen::flush() –> void

has_job_completed(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job: protocols::jd3::LarvalJob) → bool

C++: protocols::jd3::standard::StandardJobQueen::has_job_completed(class std::shared_ptr<const class protocols::jd3::LarvalJob>) –> bool

job_def_complex_type_name(type: str) → str

Naming function for the complexTypes in the job-definition XSD

C++: protocols::jd3::standard::StandardJobQueen::job_def_complex_type_name(const class std::basic_string<char> &) –> std::string

job_definition_xsd(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → str

The %StandardJobQueen assembles the XSD from virtual functions she invokes on

the derived %JobQueen: append_job_tag_subelements, append_common_tag_subelements, and add_option/add_options.

C++: protocols::jd3::standard::StandardJobQueen::job_definition_xsd() const –> std::string

job_results_that_should_be_discarded(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t

C++: protocols::jd3::standard::StandardJobQueen::job_results_that_should_be_discarded() –> class std::list<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

jobs_that_should_be_output(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_std_allocator_std_shared_ptr_protocols_jd3_output_OutputSpecification_t

C++: protocols::jd3::standard::StandardJobQueen::jobs_that_should_be_output() –> class std::list<class std::shared_ptr<class protocols::jd3::output::OutputSpecification>, class std::allocator<class std::shared_ptr<class protocols::jd3::output::OutputSpecification> > >

larval_job_needed_for_completed_job_summary(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → bool

The SJQ needs the larval job in order to create the OutputSpecification for jobs

that should be output. Derived JobQueens should only override this method if they are not using the PoseOutputters that the SJQ is using or if are themselves tracking the LarvalJobOPs for currently-running jobs (a potentially memory-hogging operation, depending on the number of jobs run at once?)

C++: protocols::jd3::standard::StandardJobQueen::larval_job_needed_for_completed_job_summary() const –> bool

larval_job_needed_for_note_job_completed(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → bool

C++: protocols::jd3::standard::StandardJobQueen::larval_job_needed_for_note_job_completed() const –> bool

mark_job_as_having_begun(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job: protocols::jd3::LarvalJob) → None

C++: protocols::jd3::standard::StandardJobQueen::mark_job_as_having_begun(class std::shared_ptr<const class protocols::jd3::LarvalJob>) –> void

note_job_completed(*args, **kwargs)

Overloaded function.

1. note_job_completed(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job: protocols::jd3::LarvalJob, status: pyrosetta.rosetta.protocols.jd3.JobStatus, nresults: int) -> None

C++: protocols::jd3::standard::StandardJobQueen::note_job_completed(class std::shared_ptr<const class protocols::jd3::LarvalJob>, enum protocols::jd3::JobStatus, unsigned long) –> void

2. note_job_completed(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job_id: int, status: pyrosetta.rosetta.protocols.jd3.JobStatus, nresults: int) -> None

C++: protocols::jd3::standard::StandardJobQueen::note_job_completed(unsigned long, enum protocols::jd3::JobStatus, unsigned long) –> void

resource_definition_xsd(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → str

C++: protocols::jd3::standard::StandardJobQueen::resource_definition_xsd() const –> std::string

result_outputter(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, spec: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification) → pyrosetta.rosetta.protocols.jd3.output.ResultOutputter

Return the bag of of PoseOutputters (in the form of a MultipleOutputter) for the

Pose that has been requested and specified by a particular OutputSpecification; this function guarantees that for each individual outputter-name (respecting the JD-provided filename suffix) that a separate set of PoseOutputters are returned so that multiple threads can potentially output at the same time.

C++: protocols::jd3::standard::StandardJobQueen::result_outputter(const class protocols::jd3::output::OutputSpecification &) –> class std::shared_ptr<class protocols::jd3::output::ResultOutputter>