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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  compare_job_nodes
 
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  JGJobNode
 
class  JGResultNode
 
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  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  JobDirectedEdge
 A run-of-the-mill directed edge to use in JobDigraphs. 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  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  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  JobOutputWriter
 JobOutputWriter class is responsible for taking data out of the JobOutput object and writing it to some sort of output destination (a file, or a database). 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  JQKey
 This key can be used by to delineate other classes to store/maintain data used by the JQ. 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< LarvalJobOPLarvalJobs
 
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

using protocols::jd3::GlobalJobID = typedef utility::StrongSize< struct GlobalJobID_ >
typedef utility::pointer::shared_ptr< InnerLarvalJob const > protocols::jd3::InnerLarvalJobCOP
typedef utility::pointer::shared_ptr< InnerLarvalJob > protocols::jd3::InnerLarvalJobOP
typedef utility::pointer::shared_ptr< InputSource const > protocols::jd3::InputSourceCOP
typedef utility::pointer::shared_ptr< InputSource > protocols::jd3::InputSourceOP
typedef utility::vector1< InputSourceOP > protocols::jd3::InputSources
using protocols::jd3::JGJobNodeAP = typedef utility::pointer::weak_ptr< JGJobNode >
using protocols::jd3::JGJobNodeCAP = typedef utility::pointer::weak_ptr< JGJobNode const >
using protocols::jd3::JGJobNodeCOP = typedef utility::pointer::shared_ptr< JGJobNode const >
using protocols::jd3::JGJobNodeOP = typedef utility::pointer::shared_ptr< JGJobNode >
using protocols::jd3::JGResultNodeAP = typedef utility::pointer::weak_ptr< JGResultNode >
using protocols::jd3::JGResultNodeCAP = typedef utility::pointer::weak_ptr< JGResultNode const >
using protocols::jd3::JGResultNodeCOP = typedef utility::pointer::shared_ptr< JGResultNode const >
using protocols::jd3::JGResultNodeOP = typedef utility::pointer::shared_ptr< JGResultNode >
typedef utility::pointer::shared_ptr< Job const > protocols::jd3::JobCOP
using protocols::jd3::JobDAGNodeID = typedef utility::StrongSize< struct JobDAGNodeID_ >
typedef utility::pointer::shared_ptr< JobDigraph const > protocols::jd3::JobDigraphCOP
typedef utility::pointer::shared_ptr< JobDigraph > protocols::jd3::JobDigraphOP
typedef utility::pointer::shared_ptr< JobDistributor const > protocols::jd3::JobDistributorCOP
typedef utility::pointer::shared_ptr< JobDistributor > protocols::jd3::JobDistributorOP
using protocols::jd3::JobGenealogistCOP = typedef utility::pointer::shared_ptr< JobGenealogist const >
using protocols::jd3::JobGenealogistOP = typedef utility::pointer::shared_ptr< JobGenealogist >
typedef utility::pointer::shared_ptr< Job > protocols::jd3::JobOP
typedef utility::pointer::shared_ptr< JobQueen const > protocols::jd3::JobQueenCOP
typedef utility::pointer::shared_ptr< JobQueen > protocols::jd3::JobQueenOP
typedef utility::pointer::shared_ptr< JobResult const > protocols::jd3::JobResultCOP

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.

typedef utility::pointer::shared_ptr< JobResult > protocols::jd3::JobResultOP
typedef utility::pointer::shared_ptr< JobSummary const > protocols::jd3::JobSummaryCOP
typedef utility::pointer::shared_ptr< JobSummary > protocols::jd3::JobSummaryOP
typedef utility::pointer::shared_ptr< JobTracker const > protocols::jd3::JobTrackerCOP
typedef utility::pointer::shared_ptr< JobTracker > protocols::jd3::JobTrackerOP
typedef utility::pointer::shared_ptr< LarvalJob const > protocols::jd3::LarvalJobCOP
typedef utility::pointer::shared_ptr< LarvalJob > protocols::jd3::LarvalJobOP
using protocols::jd3::LocalJobID = typedef utility::StrongSize< struct LocalJobID_ >
using protocols::jd3::NStructIndex = typedef utility::StrongSize< struct NStructIndex_ >
using protocols::jd3::PrelimJobNodeID = typedef utility::StrongSize< struct PrelimJobNodeID_ >
using protocols::jd3::ResultIndex = typedef utility::StrongSize< struct ResultIndex_ >
typedef utility::pointer::shared_ptr< VanillaJobDistributor const > protocols::jd3::VanillaJobDistributorCOP
typedef utility::pointer::shared_ptr< VanillaJobDistributor > protocols::jd3::VanillaJobDistributorOP

Enumeration Type Documentation

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

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().

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

core::Size protocols::jd3::nstruct_for_job ( utility::tag::TagCOP  job_tag)
std::ostream& protocols::jd3::operator<< ( std::ostream &  out,
const InnerLarvalJob &  inner_job 
)
std::ostream & protocols::jd3::operator<< ( std::ostream &  out,
const LarvalJob &  job 
)
utility::options::OptionTypes protocols::jd3::option_type_from_key ( utility::options::OptionKey const &  key)
utility::options::OptionCollectionOP protocols::jd3::options_for_job ( utility::options::OptionKeyList const &  option_keys,
InnerLarvalJob const &  inner_job,
utility::tag::TagCOP  common_block_tags 
)
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 
)
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().

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 ==.

void protocols::jd3::print_job_template ( )

Prints the job template to a Tracer.

References TR().

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