protocols::rotamer_recovery Namespace Reference

Classes
class	RotamerRecovery
class	RRProtocolCreator
	The Creator class is responsible for creating a particular mover class. More...
class	RRProtocolReferenceStructureCreator
class	RRProtocolRTMinCreator
class	RRProtocolRotamerTrialsCreator
class	RRProtocolMinPackCreator
class	RRProtocolPackRotamersCreator
class	RRProtocolRelaxCreator
class	RRProtocolMoverCreator
class	RRComparerCreator
	The Creator class is responsible for creating a particular mover class. More...
class	RRComparerAutomorphicRMSDCreator
class	RRComparerRotBinsCreator
class	RRComparerChiDiffCreator
class	RRComparerElecDensDiffCreator
class	RRReporterCreator
	The Creator class is responsible for creating a particular mover class. More...
class	RRReporterSimpleCreator
class	RRReporterHumanCreator
class	RRReporterSQLiteCreator
class	RotamerRecoveryFactory
	Create Rotamer_Recovery Reporters. More...
class	RotamerRecoveryRegistrator
	This templated class will register an instance of an RotamerRecoveryCreator (class T) with the RotamerRecoveryFactory. It will ensure that no RotamerRecoveryCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	RotamerRecoveryMover
class	RotamerRecoveryMoverCreator
class	RRComparer
	The comparison functionality for the rotamer recovery test. More...
class	RRComparerRotBins
class	RRComparerChiDiff
class	RRComparerAutomorphicRMSD
class	RRComparerElecDensDiff
class	RRProtocol
	The protocol to run to compute the rotamer recovery the rotamer recovery test. More...
class	RRProtocolMinPack
class	RRProtocolMover
class	RRProtocolPackRotamers
class	RRProtocolReferenceStructure
class	RRProtocolRelax
class	RRProtocolRotamerTrials
class	RRProtocolRTMin
class	RRReporter
	The reporting functionality for the rotamer recovery test. More...
class	RRReporterSimple
class	PerNativeRRReporterHuman
class	RRReporterHuman
	The reporting functionality for the rotamer recovery test in a human readable format. More...
class	RRReporterSQLite

Typedefs
typedef utility::pointer::shared_ptr< RotamerRecovery >	RotamerRecoveryOP
typedef utility::pointer::shared_ptr< RotamerRecovery const >	RotamerRecoveryCOP
typedef utility::pointer::shared_ptr< RRProtocolCreator >	RRProtocolCreatorOP
typedef utility::pointer::shared_ptr< RRProtocolCreator const >	RRProtocolCreatorCOP
typedef utility::pointer::shared_ptr< RRComparerCreator >	RRComparerCreatorOP
typedef utility::pointer::shared_ptr< RRComparerCreator const >	RRComparerCreatorCOP
typedef utility::pointer::shared_ptr< RRReporterCreator >	RRReporterCreatorOP
typedef utility::pointer::shared_ptr< RRReporterCreator const >	RRReporterCreatorCOP
typedef utility::pointer::shared_ptr< RotamerRecoveryFactory >	RotamerRecoveryFactoryOP
typedef utility::pointer::shared_ptr< RotamerRecoveryFactory const >	RotamerRecoveryFactoryCOP
typedef utility::pointer::shared_ptr< RotamerRecoveryMover >	RotamerRecoveryMoverOP
typedef utility::pointer::shared_ptr< RotamerRecoveryMover const >	RotamerRecoveryMoverCOP
typedef utility::pointer::shared_ptr< RRComparer >	RRComparerOP
typedef utility::pointer::shared_ptr< RRComparer const >	RRComparerCOP
typedef utility::pointer::shared_ptr< RRComparerRotBins >	RRComparerRotBinsOP
typedef utility::pointer::shared_ptr< RRComparerRotBins const >	RRComparerRotBinsCOP
typedef utility::pointer::shared_ptr< RRComparerChiDiff >	RRComparerChiDiffOP
typedef utility::pointer::shared_ptr< RRComparerChiDiff const >	RRComparerChiDiffCOP
typedef utility::pointer::shared_ptr< RRComparerAutomorphicRMSD >	RRComparerAutomorphicRMSDOP
typedef utility::pointer::shared_ptr< RRComparerAutomorphicRMSD const >	RRComparerAutomorphicRMSDCOP
typedef utility::pointer::shared_ptr< RRComparerElecDensDiff >	RRComparerElecDensDiffOP
typedef utility::pointer::shared_ptr< RRComparerElecDensDiff const >	RRComparerElecDensDiffCOP
typedef utility::pointer::shared_ptr< RRProtocol >	RRProtocolOP
typedef utility::pointer::shared_ptr< RRProtocol const >	RRProtocolCOP
typedef utility::pointer::shared_ptr< RRProtocolMinPack >	RRProtocolMinPackOP
typedef utility::pointer::shared_ptr< RRProtocolMinPack const >	RRProtocolMinPackCOP
typedef utility::pointer::shared_ptr< RRProtocolMover >	RRProtocolMoverOP
typedef utility::pointer::shared_ptr< RRProtocolMover const >	RRProtocolMoverCOP
typedef utility::pointer::shared_ptr< RRProtocolPackRotamers >	RRProtocolPackRotamersOP
typedef utility::pointer::shared_ptr< RRProtocolPackRotamers const >	RRProtocolPackRotamersCOP
typedef utility::pointer::shared_ptr< RRProtocolReferenceStructure >	RRProtocolReferenceStructureOP
typedef utility::pointer::shared_ptr< RRProtocolReferenceStructure const >	RRProtocolReferenceStructureCOP
typedef utility::pointer::shared_ptr< RRProtocolRelax >	RRProtocolRelaxOP
typedef utility::pointer::shared_ptr< RRProtocolRelax const >	RRProtocolRelaxCOP
typedef utility::pointer::shared_ptr< RRProtocolRotamerTrials >	RRProtocolRotamerTrialsOP
typedef utility::pointer::shared_ptr< RRProtocolRotamerTrials const >	RRProtocolRotamerTrialsCOP
typedef utility::pointer::shared_ptr< RRProtocolRTMin >	RRProtocolRTMinOP
typedef utility::pointer::shared_ptr< RRProtocolRTMin const >	RRProtocolRTMinCOP
typedef utility::pointer::shared_ptr< RRReporter >	RRReporterOP
typedef utility::pointer::shared_ptr< RRReporter const >	RotamerReporterCOP
typedef utility::pointer::shared_ptr< RRReporterSimple >	RRReporterSimpleOP
typedef utility::pointer::shared_ptr< RRReporterSimple const >	RotamerReporterSimpleCOP
typedef utility::pointer::shared_ptr< PerNativeRRReporterHuman >	PerNativeRRReporterHumanOP
typedef utility::pointer::shared_ptr< PerNativeRRReporterHuman const >	PerNativeRRReporterHumanCOP
typedef utility::pointer::shared_ptr< RRReporterHuman >	RRReporterHumanOP
typedef utility::pointer::shared_ptr< RRReporterHuman const >	RRReporterHumanCOP
typedef utility::pointer::shared_ptr< RRReporterSQLite >	RRReporterSQLiteOP
typedef utility::pointer::shared_ptr< RRReporterSQLite const >	RotamerReporterSQLiteCOP

Enumerations
enum	OutputLevel { OL_full = 1 , OL_features , OL_none }

Functions
static Tracer	TR ("protocol.rotamer_recovery.RotamerRecovery")
static basic::Tracer	tr ("protocols.rotamer_recovery.RotamerRecoveryFactory")
static Tracer	TR ("protocol.rotamer_recovery.RotamerRecoveryMover")
static Tracer	TR ("protocol.moves.RRComparer")
static Tracer	TR ("protocol.moves.RRComparerAutomorphicRMSD")
static Tracer	TR ("protocol.moves.RRComparerElecDensDiff")
static Tracer	TR ("protocol.moves.RRProtocol")
static Tracer	TR ("protocol.moves.RRProtocolMinPack")
static Tracer	TR ("protocol.rotamer_recovery.RRProtocolMover")
static Tracer	TR ("protocol.moves.RRProtocolPackRotamers")
static Tracer	TR ("protocol.rotamer_recovery.RRProtocolReferenceStructure")
static Tracer	TR ("protocol.moves.RRProtocolRelax")
static Tracer	TR ("protocol.moves.RRProtocolRotamerTrials")
static Tracer	TR ("protocol.moves.RRProtocolRTMin")
static Tracer	TR ("protocol.rotamer_recovery.RRReporter")
static Tracer	TR ("protocol.rotamer_recovery.RRReporterHuman")
static Tracer	TR ("protocols.rotamer_recovery.RRReporterSQLite")

Typedef Documentation

PerNativeRRReporterHumanCOP

typedef utility::pointer::shared_ptr< PerNativeRRReporterHuman const > protocols::rotamer_recovery::PerNativeRRReporterHumanCOP

PerNativeRRReporterHumanOP

typedef utility::pointer::shared_ptr< PerNativeRRReporterHuman > protocols::rotamer_recovery::PerNativeRRReporterHumanOP

RotamerRecoveryCOP

typedef utility::pointer::shared_ptr< RotamerRecovery const > protocols::rotamer_recovery::RotamerRecoveryCOP

RotamerRecoveryFactoryCOP

typedef utility::pointer::shared_ptr< RotamerRecoveryFactory const > protocols::rotamer_recovery::RotamerRecoveryFactoryCOP

RotamerRecoveryFactoryOP

typedef utility::pointer::shared_ptr< RotamerRecoveryFactory > protocols::rotamer_recovery::RotamerRecoveryFactoryOP

RotamerRecoveryMoverCOP

typedef utility::pointer::shared_ptr< RotamerRecoveryMover const > protocols::rotamer_recovery::RotamerRecoveryMoverCOP

RotamerRecoveryMoverOP

typedef utility::pointer::shared_ptr< RotamerRecoveryMover > protocols::rotamer_recovery::RotamerRecoveryMoverOP

RotamerRecoveryOP

typedef utility::pointer::shared_ptr< RotamerRecovery > protocols::rotamer_recovery::RotamerRecoveryOP

RotamerReporterCOP

typedef utility::pointer::shared_ptr< RRReporter const > protocols::rotamer_recovery::RotamerReporterCOP

RotamerReporterSimpleCOP

typedef utility::pointer::shared_ptr< RRReporterSimple const > protocols::rotamer_recovery::RotamerReporterSimpleCOP

RotamerReporterSQLiteCOP

typedef utility::pointer::shared_ptr< RRReporterSQLite const > protocols::rotamer_recovery::RotamerReporterSQLiteCOP

RRComparerAutomorphicRMSDCOP

typedef utility::pointer::shared_ptr< RRComparerAutomorphicRMSD const > protocols::rotamer_recovery::RRComparerAutomorphicRMSDCOP

RRComparerAutomorphicRMSDOP

typedef utility::pointer::shared_ptr< RRComparerAutomorphicRMSD > protocols::rotamer_recovery::RRComparerAutomorphicRMSDOP

RRComparerChiDiffCOP

typedef utility::pointer::shared_ptr< RRComparerChiDiff const > protocols::rotamer_recovery::RRComparerChiDiffCOP

RRComparerChiDiffOP

typedef utility::pointer::shared_ptr< RRComparerChiDiff > protocols::rotamer_recovery::RRComparerChiDiffOP

RRComparerCOP

typedef utility::pointer::shared_ptr< RRComparer const > protocols::rotamer_recovery::RRComparerCOP

RRComparerCreatorCOP

typedef utility::pointer::shared_ptr< RRComparerCreator const > protocols::rotamer_recovery::RRComparerCreatorCOP

RRComparerCreatorOP

typedef utility::pointer::shared_ptr< RRComparerCreator > protocols::rotamer_recovery::RRComparerCreatorOP

RRComparerElecDensDiffCOP

typedef utility::pointer::shared_ptr< RRComparerElecDensDiff const > protocols::rotamer_recovery::RRComparerElecDensDiffCOP

RRComparerElecDensDiffOP

typedef utility::pointer::shared_ptr< RRComparerElecDensDiff > protocols::rotamer_recovery::RRComparerElecDensDiffOP

RRComparerOP

typedef utility::pointer::shared_ptr< RRComparer > protocols::rotamer_recovery::RRComparerOP

RRComparerRotBinsCOP

typedef utility::pointer::shared_ptr< RRComparerRotBins const > protocols::rotamer_recovery::RRComparerRotBinsCOP

RRComparerRotBinsOP

typedef utility::pointer::shared_ptr< RRComparerRotBins > protocols::rotamer_recovery::RRComparerRotBinsOP

RRProtocolCOP

typedef utility::pointer::shared_ptr< RRProtocol const > protocols::rotamer_recovery::RRProtocolCOP

RRProtocolCreatorCOP

typedef utility::pointer::shared_ptr< RRProtocolCreator const > protocols::rotamer_recovery::RRProtocolCreatorCOP

RRProtocolCreatorOP

typedef utility::pointer::shared_ptr< RRProtocolCreator > protocols::rotamer_recovery::RRProtocolCreatorOP

RRProtocolMinPackCOP

typedef utility::pointer::shared_ptr< RRProtocolMinPack const > protocols::rotamer_recovery::RRProtocolMinPackCOP

RRProtocolMinPackOP

typedef utility::pointer::shared_ptr< RRProtocolMinPack > protocols::rotamer_recovery::RRProtocolMinPackOP

RRProtocolMoverCOP

typedef utility::pointer::shared_ptr< RRProtocolMover const > protocols::rotamer_recovery::RRProtocolMoverCOP

RRProtocolMoverOP

typedef utility::pointer::shared_ptr< RRProtocolMover > protocols::rotamer_recovery::RRProtocolMoverOP

RRProtocolOP

typedef utility::pointer::shared_ptr< RRProtocol > protocols::rotamer_recovery::RRProtocolOP

RRProtocolPackRotamersCOP

typedef utility::pointer::shared_ptr< RRProtocolPackRotamers const > protocols::rotamer_recovery::RRProtocolPackRotamersCOP

RRProtocolPackRotamersOP

typedef utility::pointer::shared_ptr< RRProtocolPackRotamers > protocols::rotamer_recovery::RRProtocolPackRotamersOP

RRProtocolReferenceStructureCOP

typedef utility::pointer::shared_ptr< RRProtocolReferenceStructure const > protocols::rotamer_recovery::RRProtocolReferenceStructureCOP

RRProtocolReferenceStructureOP

typedef utility::pointer::shared_ptr< RRProtocolReferenceStructure > protocols::rotamer_recovery::RRProtocolReferenceStructureOP

RRProtocolRelaxCOP

typedef utility::pointer::shared_ptr< RRProtocolRelax const > protocols::rotamer_recovery::RRProtocolRelaxCOP

RRProtocolRelaxOP

typedef utility::pointer::shared_ptr< RRProtocolRelax > protocols::rotamer_recovery::RRProtocolRelaxOP

RRProtocolRotamerTrialsCOP

typedef utility::pointer::shared_ptr< RRProtocolRotamerTrials const > protocols::rotamer_recovery::RRProtocolRotamerTrialsCOP

RRProtocolRotamerTrialsOP

typedef utility::pointer::shared_ptr< RRProtocolRotamerTrials > protocols::rotamer_recovery::RRProtocolRotamerTrialsOP

RRProtocolRTMinCOP

typedef utility::pointer::shared_ptr< RRProtocolRTMin const > protocols::rotamer_recovery::RRProtocolRTMinCOP

RRProtocolRTMinOP

typedef utility::pointer::shared_ptr< RRProtocolRTMin > protocols::rotamer_recovery::RRProtocolRTMinOP

RRReporterCreatorCOP

typedef utility::pointer::shared_ptr< RRReporterCreator const > protocols::rotamer_recovery::RRReporterCreatorCOP

RRReporterCreatorOP

typedef utility::pointer::shared_ptr< RRReporterCreator > protocols::rotamer_recovery::RRReporterCreatorOP

RRReporterHumanCOP

typedef utility::pointer::shared_ptr< RRReporterHuman const > protocols::rotamer_recovery::RRReporterHumanCOP

RRReporterHumanOP

typedef utility::pointer::shared_ptr< RRReporterHuman > protocols::rotamer_recovery::RRReporterHumanOP

RRReporterOP

typedef utility::pointer::shared_ptr< RRReporter > protocols::rotamer_recovery::RRReporterOP

RRReporterSimpleOP

typedef utility::pointer::shared_ptr< RRReporterSimple > protocols::rotamer_recovery::RRReporterSimpleOP

RRReporterSQLiteOP

typedef utility::pointer::shared_ptr< RRReporterSQLite > protocols::rotamer_recovery::RRReporterSQLiteOP

Enumeration Type Documentation

OutputLevel

enum protocols::rotamer_recovery::OutputLevel

Enumerator
OL_full
OL_features
OL_none

Function Documentation

TR() [1/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRComparer"  )

static

TR() [2/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRComparerAutomorphicRMSD"  )

static

TR() [3/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRComparerElecDensDiff"  )

static

TR() [4/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRProtocol"  )

static

TR() [5/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRProtocolMinPack"  )

static

TR() [6/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRProtocolPackRotamers"  )

static

TR() [7/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRProtocolRelax"  )

static

TR() [8/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRProtocolRotamerTrials"  )

static

TR() [9/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.moves.RRProtocolRTMin"  )

static

TR() [10/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.rotamer_recovery.RotamerRecovery"  )

static

Referenced by protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRProtocolReferenceStructure::parse_attributes_from_tag(), protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag(), protocols::rotamer_recovery::RRProtocolReferenceStructure::run(), protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native(), protocols::rotamer_recovery::RotamerRecovery::show(), protocols::rotamer_recovery::RRReporterSimple::show(), protocols::rotamer_recovery::RRReporterHuman::show(), and protocols::rotamer_recovery::RRReporterSQLite::show().

TR() [11/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.rotamer_recovery.RotamerRecoveryMover"  )

static

TR() [12/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.rotamer_recovery.RRProtocolMover"  )

static

TR() [13/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.rotamer_recovery.RRProtocolReferenceStructure"  )

static

TR() [14/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.rotamer_recovery.RRReporter"  )

static

TR() [15/16]

static Tracer protocols::rotamer_recovery::TR ( "protocol.rotamer_recovery.RRReporterHuman"  )

static

tr()

static basic::Tracer protocols::rotamer_recovery::tr ( "protocols.rotamer_recovery.RotamerRecoveryFactory"  )

static

Referenced by protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_comparer(), protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_protocol(), and protocols::rotamer_recovery::RotamerRecoveryFactory::get_rotamer_recovery_reporter().

TR() [16/16]

static Tracer protocols::rotamer_recovery::TR ( "protocols.rotamer_recovery.RRReporterSQLite"  )

static