protocols::jd3 Namespace Reference

Namespaces
	chunk_library
	chunk_library_inputters
	dag_node_managers
	deallocation
	full_model
	full_model_inputters
	job_distributors
	job_results
	job_summaries
	jobs
	output
	pose_inputters
	pose_outputters
	standard

Classes
struct	CompletedJobOutput
	Each Job will return a JobStatus and a list of JobSummary/JobResult pairs. A pair's index in th job_results vector is used as its identifier for when the JobResult is used as input for another job, or when it is to be output by the JobQueen. More...
class	InnerLarvalJob
class	InputSource
	The InputSource is a small class for holding data about the starting Pose for a Job and where it comes from (i.e. which of the Inputters claims responsibility for creating a Pose for this instance). The "input_tag" is a string description of the input source and will be used as the "job_tag" to control output – the input tag should not include the file extension. It is perfectly reasonable for complex Inputters to subclass from InputSource to tuck more complex data in the InputSource, though, the string-string map ought to provide considerable flexibility in storing data without deriving new subclasses. More...
class	Job
	protocols::jd3::Job, which is created by the JobQueen from a LarvalJob, is responsible for executing some protocol from beginning to end in its "run" method. It must write all of its output data to the JobResult object that it creates and returns. More...
class	JobDirectedNode
	A node to use in JobDigraphs that holds information about how much work has completed for the set of jobs that it represents. More...
class	JobDirectedEdge
	A run-of-the-mill directed edge to use in JobDigraphs. More...
class	JobDigraph
	A Digraph for storing the relationship between groups of jobs, so that each node in this graph represents a group of jobs, and if the outputs from one group are inputs to another group, then a directed edge from the first group to the second group will be in the graph. The JobDistributor will run all of the jobs in the first group before any of the jobs in the second group will start. More...
class	JobDigraphUpdater
	This class defines the set of operations that a JobQueen can perform to update the JobDigraph that she originally gave to the JobDistributor. In particular, the JobQueen may only update the JobDigraph by adding new nodes to the graph (which will receive incrementally larger indexes) and then adding edges to the graph such that the head node for the edge must land on one of the newly added nodes in the graph. The JobDistributor will hand the JobQueen a JobDigraphUpdater through the JobQueen's update_job_digraph method, and in this call, the JobQueen may add as many nodes as she wishes, and as many edges that land on those new nodes, but when the method exits, those nodes petrify: the JobQueen may not add any more edges that land on those new nodes. More...
class	JobDistributor
	OK – I don't know what the division of labor between a JobDistributor base class and a JobDistributor subclass, so I'm just going to start writing a simple JobDistributor and then follow it by writing an MPI job distributor and then I'll see what shakes out. More...
class	JobDistributorFactory
class	JGJobNode
struct	compare_job_nodes
class	JGResultNode
class	JobGenealogist
struct	JobOutputIndex
	The JobOutputIndex holds the four relevant counts for describing the "name" for an output (e.g. a Pose) that is going to be written out to disk. More...
class	JQKey
	This key can be used by to delineate other classes to store/maintain data used by the JQ. More...
class	JobQueen
	The JobQueen class (think of a queen bee) has quite a few responsibilities: More...
class	JobResult
	JobResult class holds the output that's generated by a Job over the course of its execution. The JobResult is handed by the JobQueen to the JobOutputWriter objects, each of which have the opportunity to pull data out of the JobResult class. More...
class	JobSummary
	JobSummary class holds the output that's generated by a Job over the course of its execution. The JobSummary is handed by the JobQueen to the JobOutputWriter objects, each of which have the opportunity to pull data out of the JobSummary class. More...
class	JobTracker
	A simple class for tracking job progress within JD3. More...
class	LarvalJob
	protocols::jd3::LarvalJob, which is initialized by the JobQueen, during its intitialize_job_list method, is an immature form of the. It is matured into a Job that can be run by the JobQueen's mature_job method. A LarvalJob may be one of several LarvalJobs that have the same inputs, but differ in their random number seed (i.e. replicates); two jobs that share the same input are meant to point to the same "InnerLarvalJob" to avoid spending too much memory representing identical data. More...

Typedefs
typedef std::pair< JobSummaryOP, JobResultOP >	SingleJobOutputPair
typedef std::pair< core::Size, core::Size >	JobResultID
typedef utility::pointer::shared_ptr< InnerLarvalJob >	InnerLarvalJobOP
typedef utility::pointer::shared_ptr< InnerLarvalJob const >	InnerLarvalJobCOP
typedef utility::vector1< InnerLarvalJobOP >	InnerLarvalJobs
typedef utility::pointer::shared_ptr< InputSource >	InputSourceOP
typedef utility::pointer::shared_ptr< InputSource const >	InputSourceCOP
typedef utility::vector1< InputSourceOP >	InputSources
typedef utility::pointer::shared_ptr< Job >	JobOP
typedef utility::pointer::shared_ptr< Job const >	JobCOP
typedef utility::pointer::shared_ptr< VanillaJobDistributor >	VanillaJobDistributorOP
typedef utility::pointer::shared_ptr< VanillaJobDistributor const >	VanillaJobDistributorCOP
typedef utility::pointer::shared_ptr< JobDigraph >	JobDigraphOP
typedef utility::pointer::shared_ptr< JobDigraph const >	JobDigraphCOP
typedef utility::pointer::shared_ptr< JobDistributor >	JobDistributorOP
typedef utility::pointer::shared_ptr< JobDistributor const >	JobDistributorCOP
using	JGResultNodeOP = utility::pointer::shared_ptr< JGResultNode >
using	JGResultNodeCOP = utility::pointer::shared_ptr< JGResultNode const >
using	JGResultNodeAP = utility::pointer::weak_ptr< JGResultNode >
using	JGResultNodeCAP = utility::pointer::weak_ptr< JGResultNode const >
using	JGJobNodeOP = utility::pointer::shared_ptr< JGJobNode >
using	JGJobNodeCOP = utility::pointer::shared_ptr< JGJobNode const >
using	JGJobNodeAP = utility::pointer::weak_ptr< JGJobNode >
using	JGJobNodeCAP = utility::pointer::weak_ptr< JGJobNode const >
using	JobGenealogistOP = utility::pointer::shared_ptr< JobGenealogist >
using	JobGenealogistCOP = utility::pointer::shared_ptr< JobGenealogist const >
typedef utility::pointer::shared_ptr< JobQueen >	JobQueenOP
typedef utility::pointer::shared_ptr< JobQueen const >	JobQueenCOP
typedef utility::pointer::shared_ptr< JobResult >	JobResultOP
typedef utility::pointer::shared_ptr< JobResult const >	JobResultCOP
typedef utility::pointer::shared_ptr< JobSummary >	JobSummaryOP
typedef utility::pointer::shared_ptr< JobSummary const >	JobSummaryCOP
typedef utility::pointer::shared_ptr< JobTracker >	JobTrackerOP
typedef utility::pointer::shared_ptr< JobTracker const >	JobTrackerCOP
typedef utility::pointer::shared_ptr< LarvalJob >	LarvalJobOP
typedef utility::pointer::shared_ptr< LarvalJob const >	LarvalJobCOP
typedef std::list< LarvalJobOP >	LarvalJobs
using	JobDAGNodeID = utility::StrongSize< struct JobDAGNodeID_ >
using	PrelimJobNodeID = utility::StrongSize< struct PrelimJobNodeID_ >
using	GlobalJobID = utility::StrongSize< struct GlobalJobID_ >
using	LocalJobID = utility::StrongSize< struct LocalJobID_ >
using	NStructIndex = utility::StrongSize< struct NStructIndex_ >
using	ResultIndex = utility::StrongSize< struct ResultIndex_ >

Enumerations
enum	JobStatus {   jd3_job_status_success , jd3_job_previously_executed , jd3_job_status_inputs_were_bad , jd3_job_status_failed_w_exception ,   jd3_job_status_failed_retry , jd3_job_status_failed_max_retries , jd3_job_status_failed_do_not_retry }

Functions
static basic::Tracer	TR ("protocols.jd3.InnerLarvalJob")
template<class T >
bool	pointer_equals (utility::pointer::shared_ptr< T > const &first, utility::pointer::shared_ptr< T > const &second)
	Return true if either pointers point at the same object or if they point at objects that are themselves equal. Requires that class T implements operator ==. More...
std::ostream &	operator<< (std::ostream &out, const InnerLarvalJob &inner_job)
static basic::Tracer	TR ("protocols.jd3.InputSource")
static basic::Tracer	TR ("protocols.jd3.JobDistributorFactory")
std::ostream &	operator<< (std::ostream &out, const LarvalJob &job)
void	append_residue_selector_subelements (utility::tag::XMLSchemaDefinition &job_definition_xsd, utility::tag::XMLSchemaComplexTypeGenerator &job_ct_gen)
	Append Residue Selector elements for your JD file. More...
void	append_single_scorefxn_subelement (utility::tag::XMLSchemaDefinition &job_definition_xsd, utility::tag::XMLSchemaComplexTypeGenerator &job_ct_gen)
	Append the ability to have a SINGLE ScoreFunction set. More...
void	add_residue_selectors_to_datamap (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
	Add all residue selectors to a given datamap from a tag. More...
core::select::residue_selector::ResidueSelectorCOP	parse_single_residue_selector (utility::tag::TagCOP tag, std::string const &selector_name)
	Return a single residue selector from tag. More...
core::Size	nstruct_for_job (utility::tag::TagCOP job_tag)
	Get the nstruct from the job_tag, or fallback to the cmd-line. More...
utility::options::OptionCollectionOP	options_from_tag (utility::options::OptionKeyList const &option_keys, utility::tag::TagCOP job_options_tags, utility::tag::TagCOP common_block_tags)
	Create a local options collection from a tag. More...
utility::options::OptionCollectionOP	options_for_job (utility::options::OptionKeyList const &option_keys, InnerLarvalJob const &inner_job, utility::tag::TagCOP common_block_tags)
	Create a local options collection from an InnerLarvalJob. More...
void	print_job_template ()
	Prints the job template to a Tracer. More...
utility::options::OptionTypes	option_type_from_key (utility::options::OptionKey const &key)
	Get the OptionType from a key. More...
utility::tag::XMLSchemaType	value_attribute_type_for_option (utility::options::OptionTypes const &key)
	Get the XMLSchemaType for an option key. Used during SJQ's xsd parsing. More...

Typedef Documentation

GlobalJobID

using protocols::jd3::GlobalJobID = typedef utility::StrongSize< struct GlobalJobID_ >

InnerLarvalJobCOP

typedef utility::pointer::shared_ptr< InnerLarvalJob const > protocols::jd3::InnerLarvalJobCOP

InnerLarvalJobOP

typedef utility::pointer::shared_ptr< InnerLarvalJob > protocols::jd3::InnerLarvalJobOP

InnerLarvalJobs

typedef utility::vector1< InnerLarvalJobOP > protocols::jd3::InnerLarvalJobs

InputSourceCOP

typedef utility::pointer::shared_ptr< InputSource const > protocols::jd3::InputSourceCOP

InputSourceOP

typedef utility::pointer::shared_ptr< InputSource > protocols::jd3::InputSourceOP

InputSources

typedef utility::vector1< InputSourceOP > protocols::jd3::InputSources

JGJobNodeAP

using protocols::jd3::JGJobNodeAP = typedef utility::pointer::weak_ptr< JGJobNode >

JGJobNodeCAP

using protocols::jd3::JGJobNodeCAP = typedef utility::pointer::weak_ptr< JGJobNode const >

JGJobNodeCOP

using protocols::jd3::JGJobNodeCOP = typedef utility::pointer::shared_ptr< JGJobNode const >

JGJobNodeOP

using protocols::jd3::JGJobNodeOP = typedef utility::pointer::shared_ptr< JGJobNode >

JGResultNodeAP

using protocols::jd3::JGResultNodeAP = typedef utility::pointer::weak_ptr< JGResultNode >

JGResultNodeCAP

using protocols::jd3::JGResultNodeCAP = typedef utility::pointer::weak_ptr< JGResultNode const >

JGResultNodeCOP

using protocols::jd3::JGResultNodeCOP = typedef utility::pointer::shared_ptr< JGResultNode const >

JGResultNodeOP

using protocols::jd3::JGResultNodeOP = typedef utility::pointer::shared_ptr< JGResultNode >

JobCOP

typedef utility::pointer::shared_ptr< Job const > protocols::jd3::JobCOP

JobDAGNodeID

using protocols::jd3::JobDAGNodeID = typedef utility::StrongSize< struct JobDAGNodeID_ >

JobDigraphCOP

typedef utility::pointer::shared_ptr< JobDigraph const > protocols::jd3::JobDigraphCOP

JobDigraphOP

typedef utility::pointer::shared_ptr< JobDigraph > protocols::jd3::JobDigraphOP

JobDistributorCOP

typedef utility::pointer::shared_ptr< JobDistributor const > protocols::jd3::JobDistributorCOP

JobDistributorOP

typedef utility::pointer::shared_ptr< JobDistributor > protocols::jd3::JobDistributorOP

JobGenealogistCOP

using protocols::jd3::JobGenealogistCOP = typedef utility::pointer::shared_ptr< JobGenealogist const >

JobGenealogistOP

using protocols::jd3::JobGenealogistOP = typedef utility::pointer::shared_ptr< JobGenealogist >

JobOP

typedef utility::pointer::shared_ptr< Job > protocols::jd3::JobOP

JobQueenCOP

typedef utility::pointer::shared_ptr< JobQueen const > protocols::jd3::JobQueenCOP

JobQueenOP

typedef utility::pointer::shared_ptr< JobQueen > protocols::jd3::JobQueenOP

JobResultCOP

typedef utility::pointer::shared_ptr< JobResult const > protocols::jd3::JobResultCOP

JobResultID

typedef std::pair< core::Size, core::Size > protocols::jd3::JobResultID

The first entry in this pair is the Job id; the second entry is the index for a particular job-output-pair in the CompletedJobOutput vector. E.g., the 5th JobSummary/JobResult pair for Job 132 would be identified by the pair { 132, 5 }. A JobResultID is exactly the same thing, but is given another name for when the JobQueen is trying to indicate which JobResult of all the JobSummary/JobResult pairs that she is interested in.

JobResultOP

typedef utility::pointer::shared_ptr< JobResult > protocols::jd3::JobResultOP

JobSummaryCOP

typedef utility::pointer::shared_ptr< JobSummary const > protocols::jd3::JobSummaryCOP

JobSummaryOP

typedef utility::pointer::shared_ptr< JobSummary > protocols::jd3::JobSummaryOP

JobTrackerCOP

typedef utility::pointer::shared_ptr< JobTracker const > protocols::jd3::JobTrackerCOP

JobTrackerOP

typedef utility::pointer::shared_ptr< JobTracker > protocols::jd3::JobTrackerOP

LarvalJobCOP

typedef utility::pointer::shared_ptr< LarvalJob const > protocols::jd3::LarvalJobCOP

LarvalJobOP

typedef utility::pointer::shared_ptr< LarvalJob > protocols::jd3::LarvalJobOP

LarvalJobs

typedef std::list< LarvalJobOP > protocols::jd3::LarvalJobs

LocalJobID

using protocols::jd3::LocalJobID = typedef utility::StrongSize< struct LocalJobID_ >

NStructIndex

using protocols::jd3::NStructIndex = typedef utility::StrongSize< struct NStructIndex_ >

PrelimJobNodeID

using protocols::jd3::PrelimJobNodeID = typedef utility::StrongSize< struct PrelimJobNodeID_ >

ResultIndex

using protocols::jd3::ResultIndex = typedef utility::StrongSize< struct ResultIndex_ >

SingleJobOutputPair

typedef std::pair< JobSummaryOP, JobResultOP > protocols::jd3::SingleJobOutputPair

VanillaJobDistributorCOP

typedef utility::pointer::shared_ptr< VanillaJobDistributor const > protocols::jd3::VanillaJobDistributorCOP

VanillaJobDistributorOP

typedef utility::pointer::shared_ptr< VanillaJobDistributor > protocols::jd3::VanillaJobDistributorOP

Enumeration Type Documentation

JobStatus

enum protocols::jd3::JobStatus

Enumerator
jd3_job_status_success
jd3_job_previously_executed
jd3_job_status_inputs_were_bad
jd3_job_status_failed_w_exception
jd3_job_status_failed_retry
jd3_job_status_failed_max_retries
jd3_job_status_failed_do_not_retry

Function Documentation

add_residue_selectors_to_datamap()

void protocols::jd3::add_residue_selectors_to_datamap	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

Add all residue selectors to a given datamap from a tag.

References protocols::parser::ResidueSelectorLoader::load_data().

Referenced by parse_single_residue_selector().

append_residue_selector_subelements()

void protocols::jd3::append_residue_selector_subelements	(	utility::tag::XMLSchemaDefinition &	job_definition_xsd,
		utility::tag::XMLSchemaComplexTypeGenerator &	job_ct_gen
	)

Append Residue Selector elements for your JD file.

References protocols::parser::ResidueSelectorLoader::loader_name(), protocols::parser::ResidueSelectorLoader::provide_xml_schema(), and protocols::parser::ResidueSelectorLoader::res_selector_loader_ct_namer().

append_single_scorefxn_subelement()

void protocols::jd3::append_single_scorefxn_subelement	(	utility::tag::XMLSchemaDefinition &	job_definition_xsd,
		utility::tag::XMLSchemaComplexTypeGenerator &	job_ct_gen
	)

Append the ability to have a SINGLE ScoreFunction set.

Used to have the scorefunction defined for the entire job.

References protocols::parser::ScoreFunctionLoader::provide_xml_schema(), and protocols::parser::ScoreFunctionLoader::score_function_loader_ct_namer().

nstruct_for_job()

core::Size protocols::jd3::nstruct_for_job

(

utility::tag::TagCOP

job_tag

)

Get the nstruct from the job_tag, or fallback to the cmd-line.

the nstruct count is taken from either the Job tag, or the command line. "nstruct" is not a valid option to be provided in the <Options> element and so we do not have to worry about passing in as a parameter a local OptionCollection object for this job.

Referenced by protocols::jd3::chunk_library::ChunkLibraryJobQueen::determine_preliminary_job_list_from_command_line(), protocols::jd3::full_model::FullModelJobQueen::determine_preliminary_job_list_from_command_line(), protocols::jd3::standard::StandardJobQueen::determine_preliminary_job_list_from_command_line(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::determine_preliminary_job_list_from_xml_file(), protocols::jd3::full_model::FullModelJobQueen::determine_preliminary_job_list_from_xml_file(), and protocols::jd3::standard::StandardJobQueen::determine_preliminary_job_list_from_xml_file().

operator<<() [1/2]

std::ostream& protocols::jd3::operator<<	(	std::ostream &	out,
		const InnerLarvalJob &	inner_job
	)

operator<<() [2/2]

std::ostream & protocols::jd3::operator<<	(	std::ostream &	out,
		const LarvalJob &	job
	)

References core::conformation::membrane::out, and protocols::jd3::LarvalJob::show().

option_type_from_key()

utility::options::OptionTypes protocols::jd3::option_type_from_key

(

utility::options::OptionKey const &

key

)

Get the OptionType from a key.

Referenced by protocols::jd3::standard::StandardJobQueen::job_definition_xsd(), and options_from_tag().

options_for_job()

utility::options::OptionCollectionOP protocols::jd3::options_for_job	(	utility::options::OptionKeyList const &	option_keys,
		InnerLarvalJob const &	inner_job,
		utility::tag::TagCOP	common_block_tags
	)

Create a local options collection from an InnerLarvalJob.

References protocols::jd3::InnerLarvalJob::jobdef_tag(), and options_from_tag().

Referenced by protocols::jd3::chunk_library::ChunkLibraryJobQueen::create_and_store_output_specification_for_job_result(), protocols::jd3::full_model::FullModelJobQueen::create_and_store_output_specification_for_job_result(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::has_job_previously_been_output(), protocols::jd3::full_model::FullModelJobQueen::has_job_previously_been_output(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::mature_larval_job(), protocols::jd3::full_model::FullModelJobQueen::mature_larval_job(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::note_job_completed(), protocols::jd3::full_model::FullModelJobQueen::note_job_completed(), protocols::jd3::standard::StandardJobQueen::options_for_job(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::pose_outputter_for_job(), and protocols::jd3::full_model::FullModelJobQueen::pose_outputter_for_job().

options_from_tag()

utility::options::OptionCollectionOP protocols::jd3::options_from_tag	(	utility::options::OptionKeyList const &	option_keys,
		utility::tag::TagCOP	job_options_tag,
		utility::tag::TagCOP	common_block_tags
	)

Create a local options collection from a tag.

Note that jobs specified on the command line but which the StandardJobQueen does not know about do not get set or added to the per-job options. Functions trying to read per-job options that the StandardJobQueen does not know about will die. This is intentional.

References option_type_from_key().

Referenced by protocols::jd3::chunk_library::ChunkLibraryJobQueen::determine_preliminary_job_list_from_command_line(), protocols::jd3::full_model::FullModelJobQueen::determine_preliminary_job_list_from_command_line(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::determine_preliminary_job_list_from_xml_file(), protocols::jd3::full_model::FullModelJobQueen::determine_preliminary_job_list_from_xml_file(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::options_for_job(), protocols::jd3::full_model::FullModelJobQueen::options_for_job(), options_for_job(), and protocols::jd3::standard::StandardJobQueen::options_from_tag().

parse_single_residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::jd3::parse_single_residue_selector	(	utility::tag::TagCOP	tag,
		std::string const &	selector_name
	)

Return a single residue selector from tag.

References add_residue_selectors_to_datamap(), and core::select::residue_selector::get_residue_selector().

pointer_equals()

template<class T >

bool protocols::jd3::pointer_equals	(	utility::pointer::shared_ptr< T > const &	first,
		utility::pointer::shared_ptr< T > const &	second
	)

Return true if either pointers point at the same object or if they point at objects that are themselves equal. Requires that class T implements operator ==.

print_job_template()

void protocols::jd3::print_job_template

(

)

Prints the job template to a Tracer.

References TR().

TR() [1/3]

static basic::Tracer protocols::jd3::TR ( "protocols.jd3.InnerLarvalJob"  )

static

Referenced by protocols::jd3::JobDistributorFactory::create_job_distributor(), protocols::jd3::JobGenealogist::garbage_collection(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::load_job_definition_file(), protocols::jd3::dag_node_managers::NodeManager::NodeManager(), protocols::jd3::JobGenealogist::print_all_nodes(), print_job_template(), and protocols::jd3::chunk_library::ChunkLibraryJobQueen::process_deallocation_message().

TR() [2/3]

static basic::Tracer protocols::jd3::TR ( "protocols.jd3.InputSource"  )

static

TR() [3/3]

static basic::Tracer protocols::jd3::TR ( "protocols.jd3.JobDistributorFactory"  )

static

value_attribute_type_for_option()

utility::tag::XMLSchemaType protocols::jd3::value_attribute_type_for_option

(

utility::options::OptionTypes const &

key

)

Get the XMLSchemaType for an option key. Used during SJQ's xsd parsing.

Referenced by protocols::jd3::standard::StandardJobQueen::job_definition_xsd().