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protocols::jd3::standard Namespace Reference

Classes

class  PoseOutputSpecification
 The PoseOutputSpecification. More...
 
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

typedef std::map< std::pair< std::string, std::string >, pose_outputters::PoseOutputterOP > protocols::jd3::standard::PoseOutputterMap
typedef std::map< std::pair< std::string, std::string >, pose_outputters::SecondaryPoseOutputterOP > protocols::jd3::standard::SecondaryOutputterMap
typedef numeric::DiscreteIntervalEncodingTree< core::Size > protocols::jd3::standard::SizeDIET
typedef utility::pointer::shared_ptr< StandardInnerLarvalJob const > protocols::jd3::standard::StandardInnerLarvalJobCOP
typedef utility::pointer::shared_ptr< StandardJobQueen const > protocols::jd3::standard::StandardJobQueenCOP
typedef utility::pointer::shared_ptr< StandardJobQueen > protocols::jd3::standard::StandardJobQueenOP

Function Documentation

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