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	RRProtocolMoverCreator
class	RRComparerCreator
	The Creator class is responsible for creating a particular mover class. More...
class	RRComparerAutomorphicRMSDCreator
class	RRComparerRotBinsCreator
class	RRComparerChiDiffCreator
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	RRProtocol
	The protocol to run to compute the rotamer recovery the rotamer recovery test. More...
class	RRProtocolMinPack
class	RRProtocolMover
class	RRProtocolPackRotamers
class	RRProtocolReferenceStructure
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::owning_ptr < RotamerRecovery >	RotamerRecoveryOP
typedef utility::pointer::owning_ptr < RotamerRecovery const >	RotamerRecoveryCOP
typedef utility::pointer::owning_ptr < RRProtocolCreator >	RRProtocolCreatorOP
typedef utility::pointer::owning_ptr < RRProtocolCreator const >	RRProtocolCreatorCOP
typedef utility::pointer::owning_ptr < RRComparerCreator >	RRComparerCreatorOP
typedef utility::pointer::owning_ptr < RRComparerCreator const >	RRComparerCreatorCOP
typedef utility::pointer::owning_ptr < RRReporterCreator >	RRReporterCreatorOP
typedef utility::pointer::owning_ptr < RRReporterCreator const >	RRReporterCreatorCOP
typedef utility::pointer::owning_ptr < RotamerRecoveryFactory >	RotamerRecoveryFactoryOP
typedef utility::pointer::owning_ptr < RotamerRecoveryFactory const >	RotamerRecoveryFactoryCOP
typedef utility::pointer::owning_ptr < RotamerRecoveryMover >	RotamerRecoveryMoverOP
typedef utility::pointer::owning_ptr < RotamerRecoveryMover const >	RotamerRecoveryMoverCOP
typedef utility::pointer::owning_ptr < RRComparer >	RRComparerOP
typedef utility::pointer::owning_ptr < RRComparer const >	RRComparerCOP
typedef utility::pointer::owning_ptr < RRComparerRotBins >	RRComparerRotBinsOP
typedef utility::pointer::owning_ptr < RRComparerRotBins const >	RRComparerRotBinsCOP
typedef utility::pointer::owning_ptr < RRComparerChiDiff >	RRComparerChiDiffOP
typedef utility::pointer::owning_ptr < RRComparerChiDiff const >	RRComparerChiDiffCOP
typedef utility::pointer::owning_ptr < RRComparerAutomorphicRMSD >	RRComparerAutomorphicRMSDOP
typedef utility::pointer::owning_ptr < RRComparerAutomorphicRMSD const >	RRComparerAutomorphicRMSDCOP
typedef utility::pointer::owning_ptr < RRProtocol >	RRProtocolOP
typedef utility::pointer::owning_ptr < RRProtocol const >	RRProtocolCOP
typedef utility::pointer::owning_ptr < RRProtocolMinPack >	RRProtocolMinPackOP
typedef utility::pointer::owning_ptr < RRProtocolMinPack const >	RRProtocolMinPackCOP
typedef utility::pointer::owning_ptr < RRProtocolMover >	RRProtocolMoverOP
typedef utility::pointer::owning_ptr < RRProtocolMover const >	RRProtocolMoverCOP
typedef utility::pointer::owning_ptr < RRProtocolPackRotamers >	RRProtocolPackRotamersOP
typedef utility::pointer::owning_ptr < RRProtocolPackRotamers const >	RRProtocolPackRotamersCOP
typedef utility::pointer::owning_ptr < RRProtocolReferenceStructure >	RRProtocolReferenceStructureOP
typedef utility::pointer::owning_ptr < RRProtocolReferenceStructure const >	RRProtocolReferenceStructureCOP
typedef utility::pointer::owning_ptr < RRProtocolRotamerTrials >	RRProtocolRotamerTrialsOP
typedef utility::pointer::owning_ptr < RRProtocolRotamerTrials const >	RRProtocolRotamerTrialsCOP
typedef utility::pointer::owning_ptr < RRProtocolRTMin >	RRProtocolRTMinOP
typedef utility::pointer::owning_ptr < RRProtocolRTMin const >	RRProtocolRTMinCOP
typedef utility::pointer::owning_ptr < RRReporter >	RRReporterOP
typedef utility::pointer::owning_ptr < RRReporter const >	RotamerReporterCOP
typedef utility::pointer::owning_ptr < RRReporterSimple >	RRReporterSimpleOP
typedef utility::pointer::owning_ptr < RRReporterSimple const >	RotamerReporterSimpleCOP
typedef utility::pointer::owning_ptr < PerNativeRRReporterHuman >	PerNativeRRReporterHumanOP
typedef utility::pointer::owning_ptr < PerNativeRRReporterHuman const >	PerNativeRRReporterHumanCOP
typedef utility::pointer::owning_ptr < RRReporterHuman >	RRReporterHumanOP
typedef utility::pointer::owning_ptr < RRReporterHuman const >	RRReporterHumanCOP
typedef utility::pointer::owning_ptr < RRReporterSQLite >	RRReporterSQLiteOP
typedef utility::pointer::owning_ptr < RRReporterSQLite const >	RotamerReporterSQLiteCOP

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.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.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::owning_ptr< PerNativeRRReporterHuman const > protocols::rotamer_recovery::PerNativeRRReporterHumanCOP

Definition at line 26 of file RRReporterHuman.fwd.hh.

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

Definition at line 24 of file RRReporterHuman.fwd.hh.

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

Definition at line 25 of file RotamerRecovery.fwd.hh.

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

Definition at line 25 of file RotamerRecoveryFactory.fwd.hh.

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

Definition at line 23 of file RotamerRecoveryFactory.fwd.hh.

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

Definition at line 25 of file RotamerRecoveryMover.fwd.hh.

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

Definition at line 23 of file RotamerRecoveryMover.fwd.hh.

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

Definition at line 23 of file RotamerRecovery.fwd.hh.

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

Definition at line 25 of file RRReporter.fwd.hh.

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

Definition at line 29 of file RRReporter.fwd.hh.

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

Definition at line 25 of file RRReporterSQLite.fwd.hh.

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

Definition at line 28 of file RRComparerAutomorphicRMSD.fwd.hh.

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

Definition at line 26 of file RRComparerAutomorphicRMSD.fwd.hh.

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

Definition at line 33 of file RRComparer.fwd.hh.

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

Definition at line 31 of file RRComparer.fwd.hh.

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

Definition at line 25 of file RRComparer.fwd.hh.

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

Definition at line 29 of file RotamerRecoveryCreator.fwd.hh.

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

Definition at line 27 of file RotamerRecoveryCreator.fwd.hh.

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

Definition at line 23 of file RRComparer.fwd.hh.

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

Definition at line 29 of file RRComparer.fwd.hh.

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

Definition at line 27 of file RRComparer.fwd.hh.

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

Definition at line 25 of file RRProtocol.fwd.hh.

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

Definition at line 25 of file RotamerRecoveryCreator.fwd.hh.

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

Definition at line 23 of file RotamerRecoveryCreator.fwd.hh.

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

Definition at line 25 of file RRProtocolMinPack.fwd.hh.

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

Definition at line 23 of file RRProtocolMinPack.fwd.hh.

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

Definition at line 25 of file RRProtocolMover.fwd.hh.

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

Definition at line 23 of file RRProtocolMover.fwd.hh.

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

Definition at line 23 of file RRProtocol.fwd.hh.

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

Definition at line 25 of file RRProtocolPackRotamers.fwd.hh.

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

Definition at line 23 of file RRProtocolPackRotamers.fwd.hh.

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

Definition at line 25 of file RRProtocolReferenceStructure.fwd.hh.

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

Definition at line 23 of file RRProtocolReferenceStructure.fwd.hh.

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

Definition at line 25 of file RRProtocolRotamerTrials.fwd.hh.

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

Definition at line 23 of file RRProtocolRotamerTrials.fwd.hh.

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

Definition at line 25 of file RRProtocolRTMin.fwd.hh.

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

Definition at line 23 of file RRProtocolRTMin.fwd.hh.

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

Definition at line 33 of file RotamerRecoveryCreator.fwd.hh.

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

Definition at line 31 of file RotamerRecoveryCreator.fwd.hh.

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

Definition at line 30 of file RRReporterHuman.fwd.hh.

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

Definition at line 28 of file RRReporterHuman.fwd.hh.

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

Definition at line 23 of file RRReporter.fwd.hh.

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

Definition at line 27 of file RRReporter.fwd.hh.

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

Definition at line 23 of file RRReporterSQLite.fwd.hh.

Function Documentation

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

Referenced by protocols::rotamer_recovery::RRComparerAutomorphicRMSD::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().

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

static

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

static

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

static