protocols::rotamer_recovery Namespace Reference

Classes
class	PerNativeRRReporterHuman
class	RotamerRecovery
class	RotamerRecoveryFactory
	Create Rotamer_Recovery Reporters. More...
class	RotamerRecoveryMover
class	RotamerRecoveryMoverCreator
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	RRComparer
	The comparison functionality for the rotamer recovery test. More...
class	RRComparerAutomorphicRMSD
class	RRComparerAutomorphicRMSDCreator
class	RRComparerChiDiff
class	RRComparerChiDiffCreator
class	RRComparerCreator
	The Creator class is responsible for creating a particular mover class. More...
class	RRComparerElecDensDiff
class	RRComparerElecDensDiffCreator
class	RRComparerRotBins
class	RRComparerRotBinsCreator
class	RRProtocol
	The protocol to run to compute the rotamer recovery the rotamer recovery test. More...
class	RRProtocolCreator
	The Creator class is responsible for creating a particular mover class. More...
class	RRProtocolMinPack
class	RRProtocolMinPackCreator
class	RRProtocolMover
class	RRProtocolMoverCreator
class	RRProtocolPackRotamers
class	RRProtocolPackRotamersCreator
class	RRProtocolReferenceStructure
class	RRProtocolReferenceStructureCreator
class	RRProtocolRelax
class	RRProtocolRelaxCreator
class	RRProtocolRotamerTrials
class	RRProtocolRotamerTrialsCreator
class	RRProtocolRTMin
class	RRProtocolRTMinCreator
class	RRReporter
	The reporting functionality for the rotamer recovery test. More...
class	RRReporterCreator
	The Creator class is responsible for creating a particular mover class. More...
class	RRReporterHuman
	The reporting functionality for the rotamer recovery test in a human readable format. More...
class	RRReporterHumanCreator
class	RRReporterSimple
class	RRReporterSimpleCreator
class	RRReporterSQLite
class	RRReporterSQLiteCreator

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

Variables
static Tracer	TR ("protocol.rotamer_recovery.RotamerRecovery")
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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::rotamer_recovery::OutputLevel

Enumerator
OL_full
OL_features
OL_none

Function Documentation

static thread_local 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().

Variable Documentation

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

static

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

static

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

static

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

static

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

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

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

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

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

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

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

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

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

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

static

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

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

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

static