full_model

Bindings for protocols::jd3::full_model namespace

class pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob

Bases: InnerLarvalJob

add_input_job_result_index(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, job_result_id: Tuple[int, int]) → None

Add a required input by the pair representing 1) the global index of the job

that produced the JobResult, and 2) the index of that JobResult among all the results produced by that job.

C++: protocols::jd3::InnerLarvalJob::add_input_job_result_index(struct std::pair<unsigned long, unsigned long>) –> void

append_input_source(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, setting: protocols::jd3::InputSource) → None

Append a InputSource to the vector of them

C++: protocols::jd3::InnerLarvalJob::append_input_source(class std::shared_ptr<const class protocols::jd3::InputSource>) –> void

assign(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob, : pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob) → pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob

C++: protocols::jd3::full_model::FullModelInnerLarvalJob::operator=(const class protocols::jd3::full_model::FullModelInnerLarvalJob &) –> class protocols::jd3::full_model::FullModelInnerLarvalJob &

bad(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → bool

Has this job been labeled as bad?

C++: protocols::jd3::InnerLarvalJob::bad() const –> bool

clear_input_sources(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → None

Clear the vector of InputSources

C++: protocols::jd3::InnerLarvalJob::clear_input_sources() –> void

const_data_map(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → pyrosetta.rosetta.basic.datacache.ConstDataMap

Write access to the ConstDataMap that the %InnerLarvalJob holds. The objects pointed

to by the const data map can be shared between two %InnerLarvalJobs, but the data maps themselves should not be shared.

C++: protocols::jd3::InnerLarvalJob::const_data_map() –> class basic::datacache::ConstDataMap &

input_job_result_indices(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

The list of the JobResults required to mature this %LarvalJob, by global index of the

already-executed (Lavral)Jobs

C++: protocols::jd3::InnerLarvalJob::input_job_result_indices() const –> const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &

input_source(*args, **kwargs)

Overloaded function.

1. input_source(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, setting: protocols::jd3::InputSource) -> None

Set the single InputSource for this job

C++: protocols::jd3::InnerLarvalJob::input_source(class std::shared_ptr<const class protocols::jd3::InputSource>) –> void

2. input_source(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> protocols::jd3::InputSource

Read access to the InputSource object that describes how the Pose for

this job should be constructed. Requires that there is only a single InputSource for this job.

C++: protocols::jd3::InnerLarvalJob::input_source() const –> const class protocols::jd3::InputSource &

3. input_source(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, index: int) -> protocols::jd3::InputSource

Retrieve a particular InputSource

C++: protocols::jd3::InnerLarvalJob::input_source(unsigned long) const –> const class protocols::jd3::InputSource &

input_source_cop(*args, **kwargs)

Overloaded function.

1. input_source_cop(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> protocols::jd3::InputSource

C++: protocols::jd3::InnerLarvalJob::input_source_cop() const –> const class std::shared_ptr<const class protocols::jd3::InputSource> &

2. input_source_cop(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, index: int) -> protocols::jd3::InputSource

C++: protocols::jd3::InnerLarvalJob::input_source_cop(unsigned long) const –> const class std::shared_ptr<const class protocols::jd3::InputSource> &

input_tag(*args, **kwargs)

Overloaded function.

1. input_tag(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str

Return the input tag – a string that describes the input structure, but that

is in no way a complete description of the job. The job_tag instead should be looked to as the name to use to identify information about this job: a single input structure may be used for multiple jobs.

C++: protocols::jd3::InnerLarvalJob::input_tag() const –> std::string

2. input_tag(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, setting: str) -> None

Set the input tag – if it is not set, then the InputSources will be used,

the file names / tags being concatenated together, separated by underscores.

C++: protocols::jd3::InnerLarvalJob::input_tag(const std::string &) –> void

job_node(*args, **kwargs)

Overloaded function.

1. job_node(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> int

Return the job node this InnerLarvalJob belongs to

If the Job Node has not been set, we return 0.

C++: protocols::jd3::InnerLarvalJob::job_node() const –> unsigned long

2. job_node(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, setting: int) -> None

Set the Job Node for this ILJ

C++: protocols::jd3::InnerLarvalJob::job_node(unsigned long) –> void

job_tag(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob) → str

C++: protocols::jd3::full_model::FullModelInnerLarvalJob::job_tag() const –> std::string

jobdef_tag(*args, **kwargs)

Overloaded function.

1. jobdef_tag(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> pyrosetta.rosetta.utility.tag.Tag

C++: protocols::jd3::InnerLarvalJob::jobdef_tag() const –> class std::shared_ptr<const class utility::tag::Tag>

2. jobdef_tag(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, setting: pyrosetta.rosetta.utility.tag.Tag) -> None

C++: protocols::jd3::InnerLarvalJob::jobdef_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

n_input_sources(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → int

Return the number of pose input sources for this job.

C++: protocols::jd3::InnerLarvalJob::n_input_sources() const –> unsigned long

nstruct_max(*args, **kwargs)

Overloaded function.

1. nstruct_max(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> int

The number of job replicates to be performed for this %InnerLarvalJob.

C++: protocols::jd3::InnerLarvalJob::nstruct_max() const –> unsigned long

2. nstruct_max(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, setting: int) -> None

Set the total number of Nstruct for this InnerLarvelJob (IE - how many LarvalJobs will we need?)

C++: protocols::jd3::InnerLarvalJob::nstruct_max(unsigned long) –> void

outputter(*args, **kwargs)

Overloaded function.

1. outputter(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> str

Return the outputter class; i.e. the key used by the PoseOutputterFactory

C++: protocols::jd3::InnerLarvalJob::outputter() const –> std::string

2. outputter(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, setting: str) -> None

Set the outputter class for this job; i.e. the key used by the PoseOutputterFactory

C++: protocols::jd3::InnerLarvalJob::outputter(const std::string &) –> void

same_type(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob, other: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → bool

returns true if this is the same type as other;

does not call other.same_type()

C++: protocols::jd3::full_model::FullModelInnerLarvalJob::same_type(const class protocols::jd3::InnerLarvalJob &) const –> bool

set_bad(*args, **kwargs)

Overloaded function.

1. set_bad(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) -> None

2. set_bad(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, setting: bool) -> None

Store the fact that this job is bad, for some reason or another, e.g. it has

malformed inputs.

C++: protocols::jd3::InnerLarvalJob::set_bad(bool) –> void

show(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::jd3::full_model::FullModelInnerLarvalJob::show(std::ostream &) const –> void

sources_same(self: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob, other: pyrosetta.rosetta.protocols.jd3.InnerLarvalJob) → bool

Determine if two jobs are defined with the same set of InputSources

C++: protocols::jd3::InnerLarvalJob::sources_same(const class protocols::jd3::InnerLarvalJob &) const –> bool

class pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen

Bases: JobQueen

The %FullModelJobQueen 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 %FullModelJobQueen could not perform to the derived classes.

assign(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, : pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen) → pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen

C++: protocols::jd3::full_model::FullModelJobQueen::operator=(const class protocols::jd3::full_model::FullModelJobQueen &) –> class protocols::jd3::full_model::FullModelJobQueen &

completed_job_summary(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, result_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_ResultIndex_t, summary: pyrosetta.rosetta.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::full_model::FullModelJobQueen::completed_job_summary(class std::shared_ptr<const class protocols::jd3::LarvalJob>, struct utility::StrongT<unsigned long, struct protocols::jd3::ResultIndex_>, class std::shared_ptr<class protocols::jd3::JobSummary>) –> void

create_and_set_initial_job_dag(self: pyrosetta.rosetta.protocols.jd3.JobQueen) → pyrosetta.rosetta.protocols.jd3.JobDigraph

Creates the initial job dag using create_initial_job_dag function and sets it to the JQ.

Decorator to create_initial_job_dag

C++: protocols::jd3::JobQueen::create_and_set_initial_job_dag() –> class std::shared_ptr<class protocols::jd3::JobDigraph>

create_initial_job_dag(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen) → pyrosetta.rosetta.protocols.jd3.JobDigraph

The %FullModelJobQueen provides an implementation of this function which returns

the most straight-forward DAG representing a set of jobs that have no interdependencies: a DAG with a single node and no edges.

C++: protocols::jd3::full_model::FullModelJobQueen::create_initial_job_dag() –> class std::shared_ptr<class protocols::jd3::JobDigraph>

deallocation_messages(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t

C++: protocols::jd3::full_model::FullModelJobQueen::deallocation_messages() –> class std::list<class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage>, class std::allocator<class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage> > >

determine_job_list(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, job_dag_node_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t, max_njobs: int) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t

The %FullModelJobQueen manages the process of creating the list of LarvalJobs that

will be later matured into actual jobs and run by the JobDistributor. Classes derived from the %FullModelJobQueen need answer a few virtual functions that the %FullModelJobQueen will invoke during this process.

C++: protocols::jd3::full_model::FullModelJobQueen::determine_job_list(struct utility::StrongT<unsigned long, struct protocols::jd3::JobDAGNodeID_>, unsigned long) –> class std::list<class std::shared_ptr<class protocols::jd3::LarvalJob>, class std::allocator<class std::shared_ptr<class protocols::jd3::LarvalJob> > >

determine_job_list_and_track(self: pyrosetta.rosetta.protocols.jd3.JobQueen, job_dag_node_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t, max_njobs: int) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t

Call determine_job_list in derived classes and track the jobs using the JobTracker.

Decorator to determine_job_list

C++: protocols::jd3::JobQueen::determine_job_list_and_track(struct utility::StrongT<unsigned long, struct protocols::jd3::JobDAGNodeID_>, unsigned long) –> class std::list<class std::shared_ptr<class protocols::jd3::LarvalJob>, class std::allocator<class std::shared_ptr<class protocols::jd3::LarvalJob> > >

determine_preliminary_job_list_from_xml_file(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, 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::full_model::FullModelJobQueen::determine_preliminary_job_list_from_xml_file(const std::string &) –> void

flush(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen) → None

C++: protocols::jd3::full_model::FullModelJobQueen::flush() –> void

has_job_previously_been_output(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, job: pyrosetta.rosetta.protocols.jd3.LarvalJob) → bool

C++: protocols::jd3::full_model::FullModelJobQueen::has_job_previously_been_output(class std::shared_ptr<const class protocols::jd3::LarvalJob>) –> bool

static job_def_complex_type_name(type: str) → str

Naming function for the complexTypes in the job-definition XSD

C++: protocols::jd3::full_model::FullModelJobQueen::job_def_complex_type_name(const std::string &) –> std::string

job_definition_xsd(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen) → str

The %FullModelJobQueen 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::full_model::FullModelJobQueen::job_definition_xsd() const –> std::string

job_results_that_should_be_discarded(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen) → pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t

C++: protocols::jd3::full_model::FullModelJobQueen::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.full_model.FullModelJobQueen) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t

C++: protocols::jd3::full_model::FullModelJobQueen::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> > >

note_job_completed(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, status: pyrosetta.rosetta.protocols.jd3.JobStatus, nresults: int) → None

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

note_job_completed_and_track(self: pyrosetta.rosetta.protocols.jd3.JobQueen, job: protocols::jd3::LarvalJob, status: pyrosetta.rosetta.protocols.jd3.JobStatus, nresults: int) → None

Call note_job_completed in derived classes and track the job using the JobTracker.

Decorator to note_job_completed

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

process_deallocation_message(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, message: pyrosetta.rosetta.protocols.jd3.deallocation.DeallocationMessage) → None

A deallocation message first sent to the JobDistributor on this host originating from

a remote JobQueen

C++: protocols::jd3::full_model::FullModelJobQueen::process_deallocation_message(class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage>) –> void

resource_definition_xsd(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen) → str

C++: protocols::jd3::full_model::FullModelJobQueen::resource_definition_xsd() const –> std::string

result_outputter(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, spec: protocols::jd3::output::OutputSpecification) → 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::full_model::FullModelJobQueen::result_outputter(const class protocols::jd3::output::OutputSpecification &) –> class std::shared_ptr<class protocols::jd3::output::ResultOutputter>

update_job_dag(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen, updater: pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater) → None

The %FullModelJobQueen’s implementation is to not update the JobDAG at all: the

most basic protocol defines a job DAG with only a single node.

C++: protocols::jd3::full_model::FullModelJobQueen::update_job_dag(class protocols::jd3::JobDigraphUpdater &) –> void

class pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob, rhs: pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob) → pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob

C++: protocols::jd3::full_model::FullModelPreliminaryLarvalJob::operator=(const class protocols::jd3::full_model::FullModelPreliminaryLarvalJob &) –> class protocols::jd3::full_model::FullModelPreliminaryLarvalJob &

property full_model_inputter

property inner_job

property job_options

property job_tag