protocols::jd3::standard Namespace Reference

Classes
struct	PreliminaryLarvalJob
	A PreliminaryLarvalJob is what gets created from the command-line options job_definition file for each input and specified job in the Job Definition file. More...
class	PreliminaryLarvalJobTracker
	A class for tracking the progress of all PreliminaryLarvalJobs. This tracking is partially responsible for deallocation of the input poses. More...
class	StandardInnerLarvalJob
class	StandardJobQueen
	The StandardJobQueen is meant to handle the most common form of Rosetta jobs where a protocol is applied to a single input structure to generate a single output structure. Most JobQueens in Rosetta will to derive from this JobQueen. To make the process of deriving new JobQueens easy, this class's API has been carefully designed to be easy to work with and the class itself has been designed to do as much heavy lifting as possible and to leave only the responsibilities that the StandardJobQueen could not perform to the derived classes. More...

Typedefs
typedef utility::pointer::shared_ptr< PreliminaryLarvalJobTracker >	PreliminaryLarvalJobTrackerOP
typedef utility::pointer::shared_ptr< PreliminaryLarvalJobTracker const >	PreliminaryLarvalJobTrackerCOP
typedef utility::pointer::shared_ptr< StandardInnerLarvalJob >	StandardInnerLarvalJobOP
typedef utility::pointer::shared_ptr< StandardInnerLarvalJob const >	StandardInnerLarvalJobCOP
typedef utility::vector1< StandardInnerLarvalJobOP >	StandardInnerLarvalJobs
typedef utility::pointer::shared_ptr< StandardJobQueen >	StandardJobQueenOP
typedef utility::pointer::shared_ptr< StandardJobQueen const >	StandardJobQueenCOP
typedef std::list< PreliminaryLarvalJob >	PreliminaryLarvalJobs
typedef std::map< std::string, pose_outputters::PoseOutputterOP >	RepresentativeOutputterMap
typedef std::map< std::string, pose_outputters::SecondaryPoseOutputterOP >	SecondaryRepresentativeOutputterMap
typedef std::map< std::pair< std::string, std::string >, pose_outputters::PoseOutputterOP >	PoseOutputterMap
typedef std::map< std::pair< std::string, std::string >, pose_outputters::SecondaryPoseOutputterOP >	SecondaryOutputterMap
typedef numeric::DiscreteIntervalEncodingTree< core::Size >	SizeDIET

Functions
static basic::Tracer	TR ("protocols.jd3.standard.StandardInnerLarvalJob")
std::ostream &	operator<< (std::ostream &out, const StandardInnerLarvalJob &inner_job)
std::string	perform_variable_substitution (std::string const &job_def_string)

Typedef Documentation

PoseOutputterMap

typedef std::map< std::pair< std::string, std::string >, pose_outputters::PoseOutputterOP > protocols::jd3::standard::PoseOutputterMap

PreliminaryLarvalJobs

typedef std::list< PreliminaryLarvalJob > protocols::jd3::standard::PreliminaryLarvalJobs

PreliminaryLarvalJobTrackerCOP

typedef utility::pointer::shared_ptr< PreliminaryLarvalJobTracker const > protocols::jd3::standard::PreliminaryLarvalJobTrackerCOP

PreliminaryLarvalJobTrackerOP

typedef utility::pointer::shared_ptr< PreliminaryLarvalJobTracker > protocols::jd3::standard::PreliminaryLarvalJobTrackerOP

RepresentativeOutputterMap

typedef std::map< std::string, pose_outputters::PoseOutputterOP > protocols::jd3::standard::RepresentativeOutputterMap

SecondaryOutputterMap

typedef std::map< std::pair< std::string, std::string >, pose_outputters::SecondaryPoseOutputterOP > protocols::jd3::standard::SecondaryOutputterMap

SecondaryRepresentativeOutputterMap

typedef std::map< std::string, pose_outputters::SecondaryPoseOutputterOP > protocols::jd3::standard::SecondaryRepresentativeOutputterMap

SizeDIET

typedef numeric::DiscreteIntervalEncodingTree< core::Size > protocols::jd3::standard::SizeDIET

StandardInnerLarvalJobCOP

typedef utility::pointer::shared_ptr< StandardInnerLarvalJob const > protocols::jd3::standard::StandardInnerLarvalJobCOP

StandardInnerLarvalJobOP

typedef utility::pointer::shared_ptr< StandardInnerLarvalJob > protocols::jd3::standard::StandardInnerLarvalJobOP

StandardInnerLarvalJobs

typedef utility::vector1< StandardInnerLarvalJobOP > protocols::jd3::standard::StandardInnerLarvalJobs

StandardJobQueenCOP

typedef utility::pointer::shared_ptr< StandardJobQueen const > protocols::jd3::standard::StandardJobQueenCOP

StandardJobQueenOP

typedef utility::pointer::shared_ptr< StandardJobQueen > protocols::jd3::standard::StandardJobQueenOP

Function Documentation

operator<<()

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

perform_variable_substitution()

std::string protocols::jd3::standard::perform_variable_substitution

(

std::string const &

job_def_string

)

References protocols::rosetta_scripts::RosettaScriptsParser::substitute_variables_in_stream().

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

TR()

static basic::Tracer protocols::jd3::standard::TR ( "protocols.jd3.standard.StandardInnerLarvalJob"  )

static

Referenced by protocols::jd3::standard::StandardJobQueen::determine_preliminary_job_list_from_xml_file(), protocols::jd3::standard::PreliminaryLarvalJobTracker::initialize_tracker(), protocols::jd3::standard::StandardJobQueen::load_job_definition_file(), protocols::jd3::standard::StandardJobQueen::pose_for_inner_job(), protocols::jd3::standard::StandardJobQueen::process_deallocation_message(), protocols::jd3::standard::StandardJobQueen::read_input_poses_from_command_line(), and protocols::jd3::standard::PreliminaryLarvalJobTracker::track_job_completed().