multistage_rosetta_scripts

Bindings for protocols::multistage_rosetta_scripts namespace

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.JobResultID_hash

Bases: pybind11_builtins.pybind11_object

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob

Bases: pyrosetta.rosetta.protocols.jd3.Job

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob

C++: protocols::multistage_rosetta_scripts::MRSJob::operator=(const class protocols::multistage_rosetta_scripts::MRSJob &) –> class protocols::multistage_rosetta_scripts::MRSJob &

max_num_results(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob) int

C++: protocols::multistage_rosetta_scripts::MRSJob::max_num_results() const –> unsigned long

metric_for_evaluation(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob, pose: pyrosetta.rosetta.core.pose.Pose) float

returns metric generated by the final filter of the protocol

C++: protocols::multistage_rosetta_scripts::MRSJob::metric_for_evaluation(class std::shared_ptr<class core::pose::Pose>) const –> double

parse_my_tag(*args, **kwargs)

Overloaded function.

  1. parse_my_tag(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, mover_tags_by_name: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_utility_tag_Tag_t, filter_tags_by_name: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_utility_tag_Tag_t) -> None

C++: protocols::multistage_rosetta_scripts::MRSJob::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<std::string, class std::shared_ptr<const class utility::tag::Tag>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class utility::tag::Tag> > > > &, const class std::map<std::string, class std::shared_ptr<const class utility::tag::Tag>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class utility::tag::Tag> > > > &) –> void

  1. parse_my_tag(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob, tag: pyrosetta.rosetta.utility.tag.Tag, cache: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.ParsedTagCache) -> None

C++: protocols::multistage_rosetta_scripts::MRSJob::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class std::shared_ptr<struct protocols::multistage_rosetta_scripts::ParsedTagCache>) –> void

pose(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob) pyrosetta.rosetta.core.pose.Pose

C++: protocols::multistage_rosetta_scripts::MRSJob::pose() const –> class std::shared_ptr<const class core::pose::Pose>

protocols(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob) pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t

this getter is only really intended to be used for unit tests

C++: protocols::multistage_rosetta_scripts::MRSJob::protocols() –> class std::list<struct protocols::multistage_rosetta_scripts::mover_or_filter, class std::allocator<struct protocols::multistage_rosetta_scripts::mover_or_filter> > &

run(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob) pyrosetta.rosetta.protocols.jd3.CompletedJobOutput

C++: protocols::multistage_rosetta_scripts::MRSJob::run() –> struct protocols::jd3::CompletedJobOutput

set_cluster_metric_tag(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob, tag_for_cluster_metric: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::multistage_rosetta_scripts::MRSJob::set_cluster_metric_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

set_max_num_results(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob, setting: int) None

the final mover of the protocol is allowed to return additional output poses. This value places a cap on the number of poses that can be output by that mover

C++: protocols::multistage_rosetta_scripts::MRSJob::set_max_num_results(unsigned long) –> void

set_pose(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::multistage_rosetta_scripts::MRSJob::set_pose(class std::shared_ptr<class core::pose::Pose>) –> void

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen

Bases: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen

Job Queen for MultiStage Rosetta Scripts (MRS)

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::operator=(const class protocols::multistage_rosetta_scripts::MRSJobQueen &) –> class protocols::multistage_rosetta_scripts::MRSJobQueen &

completed_job_summary(*args, **kwargs)

Overloaded function.

  1. completed_job_summary(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, job_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID__t, result_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_ResultIndex__t, summary: pyrosetta.rosetta.protocols.jd3.JobSummary) -> None

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::completed_job_summary(struct utility::StrongT<unsigned long, struct protocols::jd3::GlobalJobID_>, struct utility::StrongT<unsigned long, struct protocols::jd3::ResultIndex_>, class std::shared_ptr<class protocols::jd3::JobSummary>) –> void

  1. completed_job_summary(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, 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

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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.multistage_rosetta_scripts.MRSJobQueen) pyrosetta.rosetta.protocols.jd3.JobDigraph

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::create_initial_job_dag() –> class std::shared_ptr<class protocols::jd3::JobDigraph>

deallocation_messages(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_std_allocator_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t

Resource Management ///

C++: protocols::jd3::standard::StandardJobQueen::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.multistage_rosetta_scripts.MRSJobQueen, 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_std_allocator_std_shared_ptr_protocols_jd3_LarvalJob_t

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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_std_allocator_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.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 PreliminaryLarvalJobs; 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 std::string &) –> void

determine_validity_of_stage_tags(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) None

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::determine_validity_of_stage_tags() –> void

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

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

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

Checks the outputter to see if the job already has been output. Used for JD override behavior.

Gets the outputter from the Job, which is cached in the SJQ.

You should not need to override this method

C++: protocols::jd3::standard::StandardJobQueen::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::standard::StandardJobQueen::job_def_complex_type_name(const std::string &) –> 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.multistage_rosetta_scripts.MRSJobQueen) pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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.multistage_rosetta_scripts.MRSJobQueen) pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_std_allocator_std_shared_ptr_protocols_jd3_output_OutputSpecification_t

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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(*args, **kwargs)

Overloaded function.

  1. note_job_completed(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, job_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID__t, status: pyrosetta.rosetta.protocols.jd3.JobStatus, nresults: int, are_you_a_unit_test: bool) -> None

this was only created for the unit test. Please do not call this.

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::note_job_completed(struct utility::StrongT<unsigned long, struct protocols::jd3::GlobalJobID_>, enum protocols::jd3::JobStatus, unsigned long, bool) –> void

  1. note_job_completed(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, : int, : pyrosetta.rosetta.protocols.jd3.JobStatus, : int) -> None

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

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

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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

num_input_structs(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) int

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::num_input_structs() const –> unsigned long

num_results_to_keep_for_stage(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, stage: int) int

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::num_results_to_keep_for_stage(unsigned long) const –> unsigned long

num_stages(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) int

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::num_stages() const –> unsigned long

process_deallocation_message(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, message: pyrosetta.rosetta.protocols.jd3.deallocation.DeallocationMessage) None
A deallocation message first sent to the JobDistributor on this host originating from

a remote JobQueen. If a derived JobQueen has deallocation messages she needs to recieve, she should override derived_process_deallocation_message.

C++: protocols::jd3::standard::StandardJobQueen::process_deallocation_message(class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage>) –> 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.

You should not need to override this method.

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

stage_for_global_job_id(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, global_job_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID__t) pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID__t

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::stage_for_global_job_id(struct utility::StrongT<unsigned long, struct protocols::jd3::GlobalJobID_>) const –> struct utility::StrongT<unsigned long, struct protocols::jd3::JobDAGNodeID_>

tag_manager(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::tag_manager() const –> const class protocols::multistage_rosetta_scripts::TagManager &

update_job_dag(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, updater: pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater) None
The %StandardJobQueen’s implementation is to not update the JobDAG at all: the

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

Override this method if you have a need for updating the job dag during your protocol.

C++: protocols::jd3::standard::StandardJobQueen::update_job_dag(class protocols::jd3::JobDigraphUpdater &) –> void

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker

Bases: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker

C++: protocols::multistage_rosetta_scripts::MRSJobQueenChecker::operator=(const class protocols::multistage_rosetta_scripts::MRSJobQueenChecker &) –> class protocols::multistage_rosetta_scripts::MRSJobQueenChecker &

completed_job_summary(*args, **kwargs)

Overloaded function.

  1. completed_job_summary(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, job_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID__t, result_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_ResultIndex__t, summary: pyrosetta.rosetta.protocols.jd3.JobSummary) -> None

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::completed_job_summary(struct utility::StrongT<unsigned long, struct protocols::jd3::GlobalJobID_>, struct utility::StrongT<unsigned long, struct protocols::jd3::ResultIndex_>, class std::shared_ptr<class protocols::jd3::JobSummary>) –> void

  1. completed_job_summary(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, 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

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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.multistage_rosetta_scripts.MRSJobQueenChecker) pyrosetta.rosetta.protocols.jd3.JobDigraph

C++: protocols::multistage_rosetta_scripts::MRSJobQueenChecker::create_initial_job_dag() –> class std::shared_ptr<class protocols::jd3::JobDigraph>

deallocation_messages(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_std_allocator_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t

Resource Management ///

C++: protocols::jd3::standard::StandardJobQueen::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.multistage_rosetta_scripts.MRSJobQueenChecker, 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_std_allocator_std_shared_ptr_protocols_jd3_LarvalJob_t

C++: protocols::multistage_rosetta_scripts::MRSJobQueenChecker::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_std_allocator_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.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 PreliminaryLarvalJobs; 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 std::string &) –> void

determine_validity_of_stage_tags(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) None

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::determine_validity_of_stage_tags() –> void

estimate_number_of_bytes_needed_for_archiving(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker) int

create serialized poses for every input job and use these to predict the amount of memory required for archiving results

C++: protocols::multistage_rosetta_scripts::MRSJobQueenChecker::estimate_number_of_bytes_needed_for_archiving() –> unsigned long

static fa_and_cen_sizes_for_archives(pose: pyrosetta.rosetta.core.pose.Pose) Tuple[int, int]

C++: protocols::multistage_rosetta_scripts::MRSJobQueenChecker::fa_and_cen_sizes_for_archives(class std::shared_ptr<class core::pose::Pose>) –> struct std::pair<unsigned long, unsigned long>

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

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

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

Checks the outputter to see if the job already has been output. Used for JD override behavior.

Gets the outputter from the Job, which is cached in the SJQ.

You should not need to override this method

C++: protocols::jd3::standard::StandardJobQueen::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::standard::StandardJobQueen::job_def_complex_type_name(const std::string &) –> 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.multistage_rosetta_scripts.MRSJobQueen) pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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.multistage_rosetta_scripts.MRSJobQueen) pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_std_allocator_std_shared_ptr_protocols_jd3_output_OutputSpecification_t

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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(*args, **kwargs)

Overloaded function.

  1. note_job_completed(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, job_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID__t, status: pyrosetta.rosetta.protocols.jd3.JobStatus, nresults: int, are_you_a_unit_test: bool) -> None

this was only created for the unit test. Please do not call this.

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::note_job_completed(struct utility::StrongT<unsigned long, struct protocols::jd3::GlobalJobID_>, enum protocols::jd3::JobStatus, unsigned long, bool) –> void

  1. note_job_completed(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, : int, : pyrosetta.rosetta.protocols.jd3.JobStatus, : int) -> None

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

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

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::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

num_input_structs(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) int

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::num_input_structs() const –> unsigned long

num_results_to_keep_for_stage(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, stage: int) int

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::num_results_to_keep_for_stage(unsigned long) const –> unsigned long

num_stages(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) int

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::num_stages() const –> unsigned long

process_deallocation_message(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, message: pyrosetta.rosetta.protocols.jd3.deallocation.DeallocationMessage) None
A deallocation message first sent to the JobDistributor on this host originating from

a remote JobQueen. If a derived JobQueen has deallocation messages she needs to recieve, she should override derived_process_deallocation_message.

C++: protocols::jd3::standard::StandardJobQueen::process_deallocation_message(class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage>) –> 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.

You should not need to override this method.

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

stage_for_global_job_id(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen, global_job_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID__t) pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID__t

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::stage_for_global_job_id(struct utility::StrongT<unsigned long, struct protocols::jd3::GlobalJobID_>) const –> struct utility::StrongT<unsigned long, struct protocols::jd3::JobDAGNodeID_>

tag_manager(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager

C++: protocols::multistage_rosetta_scripts::MRSJobQueen::tag_manager() const –> const class protocols::multistage_rosetta_scripts::TagManager &

update_job_dag(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, updater: pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater) None
The %StandardJobQueen’s implementation is to not update the JobDAG at all: the

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

Override this method if you have a need for updating the job dag during your protocol.

C++: protocols::jd3::standard::StandardJobQueen::update_job_dag(class protocols::jd3::JobDigraphUpdater &) –> void

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary

Bases: pyrosetta.rosetta.protocols.jd3.job_summaries.EnergyJobSummary

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary

C++: protocols::multistage_rosetta_scripts::MRSJobSummary::operator=(const class protocols::multistage_rosetta_scripts::MRSJobSummary &) –> class protocols::multistage_rosetta_scripts::MRSJobSummary &

cluster_metric(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary) protocols::multistage_rosetta_scripts::cluster::ClusterMetric

C++: protocols::multistage_rosetta_scripts::MRSJobSummary::cluster_metric() –> class std::shared_ptr<class protocols::multistage_rosetta_scripts::cluster::ClusterMetric>

energy(*args, **kwargs)

Overloaded function.

  1. energy(self: pyrosetta.rosetta.protocols.jd3.job_summaries.EnergyJobSummary, setting: float) -> None

Set an energy of the job.

C++: protocols::jd3::job_summaries::EnergyJobSummary::energy(double) –> void

  1. energy(self: pyrosetta.rosetta.protocols.jd3.job_summaries.EnergyJobSummary) -> float

Get the energy stored in this JobSummary.

C++: protocols::jd3::job_summaries::EnergyJobSummary::energy() const –> double

extract_energy(self: pyrosetta.rosetta.protocols.jd3.job_summaries.EnergyJobSummary, pose: pyrosetta.rosetta.core.pose.Pose) None

Extract the energy fromt the Energies object of the pose

C++: protocols::jd3::job_summaries::EnergyJobSummary::extract_energy(const class core::pose::Pose &) –> void

set_cluster_metric(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary, setting: protocols::multistage_rosetta_scripts::cluster::ClusterMetric) None

C++: protocols::multistage_rosetta_scripts::MRSJobSummary::set_cluster_metric(class std::shared_ptr<class protocols::multistage_rosetta_scripts::cluster::ClusterMetric>) –> void

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap

Bases: pyrosetta.rosetta.basic.datacache.DataMap

This class does not fail when you try to add an element that already exists. Instead, it just keeps the older element.

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap

C++: protocols::multistage_rosetta_scripts::NoFailDataMap::operator=(const class protocols::multistage_rosetta_scripts::NoFailDataMap &) –> class protocols::multistage_rosetta_scripts::NoFailDataMap &

has(*args, **kwargs)

Overloaded function.

  1. has(self: pyrosetta.rosetta.basic.datacache.DataMap, type: str) -> bool

  2. has(self: pyrosetta.rosetta.basic.datacache.DataMap, type: str, name: str) -> bool

Does the data map contain an entry with a specific name in the given type?

calling this function without providing a name is just plain wrong and makes no sense and I would be changing that right now if Kale hadn’t already found out that some code relies on this bad behavior back in pull request #187

C++: basic::datacache::DataMap::has(const std::string &, const std::string &) const –> bool

has_resource(self: pyrosetta.rosetta.basic.datacache.DataMap, resource_name: str) bool

Does the data map contain a resource with the given name?

C++: basic::datacache::DataMap::has_resource(const std::string &) const –> bool

has_type(self: pyrosetta.rosetta.basic.datacache.DataMap, type: str) bool

Does the data map contain the given type?

C++: basic::datacache::DataMap::has_type(const std::string &) const –> bool

size(self: pyrosetta.rosetta.basic.datacache.DataMap) int

returns the size of the map (how many different types are in data_map_

C++: basic::datacache::DataMap::size() const –> unsigned long

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.ParsedTagCache

Bases: pybind11_builtins.pybind11_object

property data_map
property filter_tags
property input_pose_id
property mover_tags
class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID

Bases: pybind11_builtins.pybind11_object

We do not want to load all of the input poses into memory at once. Instead we use this struct to keep track of the most recent pose loaded (which is assumed to be the most likely one we are going to need next)

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID

C++: protocols::multistage_rosetta_scripts::PoseForPoseID::operator=(const struct protocols::multistage_rosetta_scripts::PoseForPoseID &) –> struct protocols::multistage_rosetta_scripts::PoseForPoseID &

property pose
property pose_id
class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.SortByLowEnergy

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.SortByLowEnergy, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.SortByLowEnergy) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.SortByLowEnergy

C++: protocols::multistage_rosetta_scripts::SortByLowEnergy::operator=(const struct protocols::multistage_rosetta_scripts::SortByLowEnergy &) –> struct protocols::multistage_rosetta_scripts::SortByLowEnergy &

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager, : pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager

C++: protocols::multistage_rosetta_scripts::TagManager::operator=(const class protocols::multistage_rosetta_scripts::TagManager &) –> class protocols::multistage_rosetta_scripts::TagManager &

generate_data_for_input_pose_id(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager, input_pose_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_PrelimJobNodeID__t) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.ParsedTagCache

C++: protocols::multistage_rosetta_scripts::TagManager::generate_data_for_input_pose_id(struct utility::StrongT<unsigned long, struct protocols::jd3::PrelimJobNodeID_>) –> class std::shared_ptr<struct protocols::multistage_rosetta_scripts::ParsedTagCache>

register_data_tags_for_input_pose_id(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager, input_pose_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_PrelimJobNodeID__t, tags_in_order: pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_std_allocator_std_shared_ptr_const_utility_tag_Tag_t) None

register all tags that are not present in common tags

C++: protocols::multistage_rosetta_scripts::TagManager::register_data_tags_for_input_pose_id(struct utility::StrongT<unsigned long, struct protocols::jd3::PrelimJobNodeID_>, const class std::list<class std::shared_ptr<const class utility::tag::Tag>, class std::allocator<class std::shared_ptr<const class utility::tag::Tag> > > &) –> void

set_common_data_tags(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager, tags_in_order: pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_std_allocator_std_shared_ptr_const_utility_tag_Tag_t) None

C++: protocols::multistage_rosetta_scripts::TagManager::set_common_data_tags(const class std::list<class std::shared_ptr<const class utility::tag::Tag>, class std::allocator<class std::shared_ptr<const class utility::tag::Tag> > > &) –> void

set_num_input_pose_ids(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager, num_input_pose_ids: int) None

C++: protocols::multistage_rosetta_scripts::TagManager::set_num_input_pose_ids(unsigned long) –> void

tag_list_for_input_pose_id(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager) pyrosetta.rosetta.std.vector_std_shared_ptr_std_list_std_shared_ptr_const_utility_tag_Tag_std_allocator_std_shared_ptr_const_utility_tag_Tag_t

C++: protocols::multistage_rosetta_scripts::TagManager::tag_list_for_input_pose_id() const –> const class std::vector<class std::shared_ptr<class std::list<class std::shared_ptr<const class utility::tag::Tag>, class std::allocator<class std::shared_ptr<const class utility::tag::Tag> > > >, class std::allocator<class std::shared_ptr<class std::list<class std::shared_ptr<const class utility::tag::Tag>, class std::allocator<class std::shared_ptr<const class utility::tag::Tag> > > > > > &

class pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter, src: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter

C++: protocols::multistage_rosetta_scripts::mover_or_filter::operator=(const struct protocols::multistage_rosetta_scripts::mover_or_filter &) –> struct protocols::multistage_rosetta_scripts::mover_or_filter &

deep_clone(self: pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter) pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter

C++: protocols::multistage_rosetta_scripts::mover_or_filter::deep_clone() –> struct protocols::multistage_rosetta_scripts::mover_or_filter

property filter
property is_mover
property mover