- t -
- T_design()
: AnchorMovers.cc
- T_perturb()
: AnchorMovers.cc
- T_refine()
: AnchorMovers.cc
- T_shared()
: AnchorMovers.cc
- TC()
: InterchainPotential.cc
- tr()
: BinaryProteinSilentStruct.cc
, CoordinateConstraint.cc
, OccludedHbondSolEnergy_onebody.cc
, IterativeFullatom.cc
, BatchJobInputter.cc
- TR()
: HPatchEnergy.cc
, OopPuckMover.cc
, OopRandomPuckMover.cc
, SurfaceEnergy.cc
, OopRandomSmallMover.cc
, PeptideStapleMover.cc
- tr()
: LazySilentFileJobInputter.cc
- TR()
: make_symmetric_task.cc
, ReturnSidechainMover.cc
, RotamerTrialsMinMover.cc
, pack_missing_sidechains.cc
, RotamerTrialsMover.cc
, SequenceProfileMover.cc
- tr()
: KinematicAbinitio.cc
, MPIFileBufJobDistributor.cc
- TR()
: util.cc
, SetReturningPackRotamersMover.cc
, PerturbChiSidechainMover.cc
, DatabaseQueryWorkUnitManager.hh
, DatabaseEntryWorkUnit.cc
, UnfoldedStateEnergyCalculatorUtil.cc
, UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc
, UnfoldedStateEnergyCalculatorJobDistributor.cc
, MembraneTopologyClaimer.cc
, ThreadSequenceOperation.cc
, SelectBySASAOperation.cc
, RestrictToTerminiOperation.cc
, RestrictToNeighborhoodOperation.cc
, RestrictToInterfaceVectorOperation.cc
, RestrictToInterfaceOperation.cc
, RestrictToAlignedSegments.cc
, RestrictResiduesToRepackingOperation.cc
, RestrictNonSurfaceToRepackingOperation.cc
, RestrictNativeResiduesOperation.cc
, RestrictInterGroupVectorOperation.cc
, RestrictIdentitiesAtAlignedPositions.cc
, RestrictChainToRepackingOperation.cc
, RestrictByCalculatorsOperation.cc
, ProteinInterfaceDesignOperation.cc
, ProteinCoreResFilter.cc
, PreventResiduesFromRepackingOperation.cc
, PreventChainFromRepackingOperation.cc
, LayerOperations.cc
, JointSequenceOperation.cc
, DesignAroundOperation.cc
, SelectResiduesByLayer.cc
, SemiExplicitWaterUnsatisfiedPolarsCalculator.cc
, SaltBridgeCalculator.cc
, PiPiCalculator.cc
, PackstatCalculator.cc
, NonlocalContactsCalculator.cc
, NeighborsByDistanceCalculator.cc
, NeighborhoodByDistanceCalculator.cc
, InterGroupNeighborsCalculator.cc
, FragQualCalculator.cc
, CatPiCalculator.cc
, BuriedUnsatisfiedPolarsCalculator.cc
, KCluster.cc
, SymSidechainMinMover.cc
, SymDockingLowRes.cc
, SymDockingHiRes.cc
, StepWiseScreener.cc
, StepWiseResidueSampler.cc
, StepWisePoseSetup.cc
, StepWiseClusterer.cc
, StepWiseRNA_VirtualRiboseSampler.cc
, StepWiseRNA_RotamerGenerator_Wrapper.cc
, StepWiseRNA_RotamerGenerator.cc
, StepWiseRNA_ResidueSampler.cc
, StepWiseRNA_PoseSetup.cc
, StepWiseRNA_Minimizer.cc
, StepWiseRNA_JobParameters_Setup.cc
, StepWiseRNA_FloatingBase_Sampler_Util.cc
, StepWiseRNA_CombineLongLoopFilterer.cc
, StepWiseRNA_Clusterer.cc
, StepWiseRNA_BaseCentroidScreener.cc
, StepWiseRNA_Base_Sugar_Rotamer.cc
, RigidBodySampler.cc
, StepWiseProteinScreener.cc
, StepWiseProteinResidueSampler.cc
, StepWiseProteinPacker.cc
, StepWiseProteinLoopBridger.cc
, StepWiseProteinCCD_Closer.cc
, RNA_TorsionMover.cc
, RNA_SWA_MonteCarloMover.cc
, RNA_O2StarMover.cc
, RNA_DeleteMover.cc
, RNA_AddOrDeleteMover.cc
, RNA_AddMover.cc
, SurfaceParameters.cc
, SurfaceOrientMover.cc
, SurfaceDockingProtocol.cc
, SlideIntoSurface.cc
, FullatomRelaxMover.cc
, CentroidRelaxMover.cc
, WobbleMover.cc
, TorsionDOFMover.cc
, TaskAwareMinMover.cc
, TailsScoreMover.cc
, SymPackRotamersMover.cc
, SymMinMover.cc
, SymDockingInitialPerturbation.cc
, SwitchResidueTypeSetMover.cc
, selection.cc
, PerturbRotamerSidechainMover.cc
, SidechainMCMover.cc
- tr()
: MPIMultiCommJobDistributor.cc
- TR()
: APBSWrapper.cc
, SidechainMover.cc
, SwitchChainOrderMover.cc
, FabConstraint.cc
- tr()
: ChemicalShiftAnisotropyEnergy.cc
, KinematicControl.cc
, PoseInputStreamJobInputter.cc
- TR()
: SiteConstraint.cc
, SiteConstraintResidues.cc
- tr()
: SilentFileJobInputter.cc
- TR()
: OopPatcher.cc
, OopMover.cc
, MonteCarloTest.cc
, MonteCarloRecover.cc
, MakePolyXMover.cc
, LoadUnboundRotMover.cc
, LoadPDBMover.cc
, HelicalPeptideLengthMover.cc
, HbsPatcher.cc
, GenericMonteCarloMover.cc
, DME_FilterMover.cc
, DesignRepackMover.cc
, ConstraintSetMover.cc
, ConstrainToIdealMover.cc
, ConsensusDesignMover.cc
, ChiralMover.cc
, RingConformationMover.cc
, BBGaussianMover.cc
, BBConRotMover.cc
, BackboneMover.cc
, AddConstraintsToCurrentConformationMover.cc
, SwapSegment.cc
, SeedFoldTree.cc
, SeededAbinitio_util.cc
, GrowPeptides.cc
, DefineMovableLoops.cc
, CloseFold.cc
, InterchainEnvEnergy.cc
, EnsembleEnergy.cc
, Interface.cc
, sasapack.cc
, util.cc
, SavePoseMover.cc
, RNA_Relaxer.cc
, RNA_ProtocolUtil.cc
, RNA_Minimizer.cc
, RNA_LoopCloser.cc
, RNA_HelixAssembler.cc
, RNA_FragmentMover.cc
, RNA_ChunkLibrary.cc
, RNA_BasePairClassifier.cc
, RotateJumpAxisMover.cc
, RollMover.cc
, RB_geometry.cc
, util.cc
, RelaxProtocolBase.cc
, Ramady.cc
, MiniRelax.cc
, FastRelax.cc
, ClassicRelax.cc
, CentroidRelax.cc
, util.cc
, ReportPSSMDifference.cc
, read_patchdock.cc
, ParserJobInputter.cc
, parse_filters.cc
, SubroutineMover.cc
, PlaceUtils.cc
, PlaceStubMover.cc
, PlaceSimultaneouslyMover.cc
, PlacementMinimizationMover.cc
, PlacementAuctionMover.cc
, InterfaceRecapitulationMover.cc
, design_utils.cc
, MultistateFitnessFunction.cc
, PNatLigPoseOptEData.cc
, MultiStatePacker.cc
, ReplicaExchangeMC.cc
, MoverStatistics.cc
, MonteCarlo.cc
, FilterMover.cc
, DsspMover.cc
, util.cc
, loopfinder.cc
, SmallMinCCDTrial.cc
, ShearMinCCDTrial.cc
, RepackTrial.cc
, LoopRefineInnerCycleContainer.cc
, LoopRefineInnerCycle.cc
, KinematicWrapper.cc
, KinematicMover.cc
, Mover_LoopHashRefine.cc
, LoopHashRelaxProtocol.cc
, RigidSearchMover.cc
, FunGroupTK.cc
, ShuffleJobDistributor.cc
, PDBJobOutputter.cc
, PDBJobInputter.cc
, FragSetLoader.cc
, FragmentReader.cc
, BluePrint.cc
, MPIWorkPoolJobDistributor.cc
, MPIWorkPartitionJobDistributor.cc
, Job.cc
, InnerMultiThreadingJob.cc
, InnerJob.cc
, FileSystemJobDistributor.cc
, FileJobOutputter.cc
, BOINCJobDistributor.cc
, AtomTreeDiffJobOutputter.cc
, WeightedFragmentSmoothTrialMover.cc
, InsertChunkMover.cc
, HybridizeProtocol.cc
, HybridizeFoldtreeDynamic.cc
, FoldTreeHybridize.cc
, DomainAssembly.cc
, ChunkTrialMover.cc
, util.cc
, GraftMoverBase.cc
, AnchoredGraftMover.cc
, VallData.cc
, TorsionFragment.cc
, VallProvider.cc
, RemodelConstraintGenerator.cc
, RemoveCsts.cc
, NtoC_RCG.cc
, utility.cc
, LayerDesignOperation.cc
, InterlockAroma.cc
, FlxbbDesign.cc
, FilterStructs.cc
, DesignTask.cc
, FloppyTailMover.cc
, FlexPepDockingProtocol.cc
, FlexPepDockingPoseMetrics.cc
, FlexPepDockingLowRes.cc
, FlexPepDockingFlags.cc
, SplineFunc.cc
, util.cc
, StrandPairing.cc
, Sheet.cc
, HSSTriplet.cc
, HelixPairing.cc
, BetaAlphaBetaMotif.cc
, SheetConstraintsRCG.cc
, SSPairPotential.cc
, NatbiasStrandPairPotential.cc
, NatbiasSheetPotential.cc
, NatbiasSecondaryStructureEnergy.cc
, NatbiasHelixPairPotential.cc
, NatbiasHelicesSheetPotential.cc
, HSPairPotential.cc
, MatchResiduesMover.cc
, MatchResidues.cc
, ParallelBetaPairingPreferenceFilter.cc
, HSSTripletFilter.cc
, HelixPairingFilter.cc
, HelixKinkFilter.cc
, Filter.cc
, BasicFilters.cc
, StructureFeatures.cc
, StrandBundleFeatures.cc
, ProtocolFeatures.cc
, HelixBundleFeatures.cc
, EnzRepackMinimize.cc
, EnzFilters.cc
, EnzdesJobInputter.cc
, util.cc
, SidechainMinMover.cc
, metrics.cc
, DockTaskFactory.cc
, DockMCMProtocol.cc
, DockMCMCycle.cc
, DockingProtocol.cc
, DockingPrepackProtocol.cc
, DockingLowResEnsemble.cc
, DockingLowRes.cc
, DockingInitialPerturbation.cc
, DockingHighResLegacy.cc
, DockingHighRes.cc
, DockingEnsemblePrepackProtocol.cc
, DockingEnsemble.cc
, DockFilters.cc
, ConformerSwitchMover.cc
, RotamerDNAHBondFilter.cc
, ddGMover.cc
, ddG_main.cc
, CoarseRNA_LoopCloser.cc
, CoarseRNA_Fragments.cc
, APCluster.cc
, MetropolisHastingsMover.cc
, pool_util.cc
, HPool.cc
, BranchAngleOptimizer.cc
, BackrubSidechainMover.cc
, BackrubMover.cc
, SnugDockProtocol.cc
, SnugDock.cc
, RefineOneCDRLoopCentroid.cc
, RefineOneCDRLoop.cc
, SquareWell2Func.cc
, ModelCDRH3.cc
, LHSnugFitLegacy.cc
, LHRepulsiveRampLegacy.cc
, LHRepulsiveRamp.cc
, H3RefineCCD.cc
, H3PerturbCCD.cc
, H3CterInsert.cc
, GraftCDRLoopsProtocol.cc
, CDRsMinPackMin.cc
, AntibodyUtil.cc
, AntibodyModelerProtocol.cc
, AntibodyInfo.cc
, Ab_TemplateInfo.cc
, Ubiquitin_E2C_Modeler.cc
, GraftMover.cc
, CDRH3Modeler.cc
, AntibodyModeler.cc
, AntibodyClass.cc
, AnchorMoversData.cc
, Anchor.cc
, PackStatMover.cc
, LoopAnalyzerMover.cc
, InterfaceAnalyzerMover.cc
, ABEGOManager.cc
, symE.cc
, ShapeComplementarityCalculator.cc
, MolecularSurfaceCalculator.cc
, sasa.cc
, RNA_ChemicalShiftPotential.cc
, PoissonBoltzmannPotential.cc
, SimplePDB.cc
, compute_holes_score.cc
, NVlookup.cc
, MMBondAngleResidueTypeParam.cc
, UnfoldedStateEnergy.cc
, PoissonBoltzmannEnergy.cc
, NMerRefEnergy.cc
, NMerPSSMEnergy.cc
, MembraneEnvSmoothEnergy.cc
, DFIRE_Energy.cc
, MembEtable.cc
, HackElecEnergy.cc
, non_scorefxn_exact_model.cc
, ExactOccludedHbondSolEnergy.cc
, FACTSPotential.cc
, MembEtable.cc
, Etable.cc
, xray_scattering.cc
- tr()
: KinematicTaskControl.cc
, SilentFileJobOutputter.cc
- TR()
: CentroidDisulfidePotential.cc
, DisulfideMatchingDatabase.cc
- tr()
: DisulfPairingLibrary.cc
- TR()
: DisulfideMatchingPotential.cc
, FullatomDisulfidePotential.cc
- tr()
: LocalCoordinateConstraint.cc
, ContactOrderEnergy.cc
, LoopJumpFoldCst.cc
, DisulfPairingsList.cc
, PairingLibrary.cc
, MembraneAbinitio.cc
, RandomSheetBuilder.cc
, SameStrand.cc
, DipolarCouplingEnergy.cc
- TR()
: RotamerLibrary.cc
, DunbrackRotamer.cc
, FixbbSimAnnealer.cc
, LineMinimizer.cc
, FoldTree.cc
, SilentFileLoader.cc
, pdb_dynamic_reader.cc
, util.cc
, SymmetryInfo.cc
, Conformation.cc
, CarbohydrateInfo.cc
, adduct_util.cc
- tr()
: util.cc
, TopologyClaimerFactory.cc
, TopologyClaimer.cc
, TopologyBroker.cc
, TemplateJumpClaimer.cc
, TemplateFragmentClaimer.cc
, StartStructClaimer.cc
, SequenceClaimer.cc
, RigidChunkClaimer.cc
, MetalloClaimer.cc
, LoopFragmentClaimer.cc
, JumpClaimer.cc
, FragmentClaimer.cc
, FoldandDockClaimer.cc
, FibrilModelingClaimer.cc
, DofClaim.cc
, DisulfJumpClaimer.cc
, DensityScoringClaimer.cc
, CutBiasClaimer.cc
, CoordConstraintClaimer.cc
, ConstraintEvaluatorWrapperCreator.cc
, ConstraintEvaluatorWrapper.cc
, ConstraintClaimer.cc
, AsymFoldandDockClaimer.cc
, SeqprofConsensusOperation.cc
, ClashCountCalculator.cc
, MatchConstraintFileInfo.cc
, EnzdesLoopsFile.cc
, EnzCstTemplateRes.cc
, EnzConstraintParameters.cc
, EnzConstraintIO.cc
, SpartaUtil.cc
, GDB.cc
, ChemicalShiftEvaluatorCreator.cc
, ANN.cc
, SidechainMoverBase.cc
, JumpRotamerSidechainMover.cc
, StructureSimilarityEvaluatorCreator.cc
, SheetFilter.cc
, ShapeComplementarityFilter.cc
, ScoreEvaluator.cc
, ScoreCutoffFilter.cc
, SAXSScoreFilter.cc
, RmsdTargetEvaluatorCreator.cc
, RmsdEvaluatorCreator.cc
, RmsdEvaluator.cc
, RGFilter.cc
, RdcTargetEvaluatorCreator.cc
, RdcSelectEvaluatorCreator.cc
, RdcEvaluatorCreator.cc
, RDC_Evaluator.cc
- TR()
: FlexPepDockingAbInitio.cc
- tr()
: PredictedBurialFnEvaluatorCreator.cc
, PoolEvaluatorCreator.cc
, PDDFScoreFilter.cc
, PalesEvaluatorCreator.cc
, PalesEvaluator.cc
, PackStatFilter.cc
, PackerNeighborGraphFilter.cc
, NativeEvaluatorCreator.cc
, JumpNrEvaluatorCreator.cc
, JScoreEvaluatorCreator.cc
, HolesFilter.cc
, ExtraScoreEvaluatorCreator.cc
, ExternalEvaluator.cc
, ContactMapEvaluatorCreator.cc
, ConstraintScoreCutoffFilter.cc
, ConservedPosMutationFilter.cc
, COFilter.cc
, ChiWellRmsdEvaluatorCreator.cc
, ChiWellRmsdEvaluator.cc
, CamShiftEvaluatorCreator.cc
, CamShiftEvaluator.cc
, AbinitioBaseFilter.cc
, ResidualDipolarCouplingRigidSegments.cc
, ResidualDipolarCouplingEnergyRigidSegments.cc
, relax_main.cc
, cst_util.cc
, StructureIndependentPeakCalibrator.cc
, StructureDependentPeakCalibrator.cc
, ResonanceList.cc
, Resonance.cc
, PeakFileFormat_xpk.cc
- TR()
: RefineBetaBarrel.cc
- tr()
: PeakFileFormat.cc
, PeakCalibrator.cc
, PeakAssignmentResidueMap.cc
, PeakAssignmentParameters.cc
, PeakAssignment.cc
, NoesyModule.cc
, MethylNames.cc
, FragsToAtomDist.cc
, FloatingResonance.cc
, DistanceScoreMover.cc
, CyanaModule.cc
, CrossPeakList.cc
, CrossPeakInfo.cc
, CrossPeak.cc
, Assignment.cc
, TrialCounter.cc
, PairingStatistics.cc
, SheetBuilder.cc
, WidthFirstSlidingWindowLoopClosure.cc
, Protocol.cc
, loopfinder.cc
, MoverContainer.cc
, ResidueCoordinateChangeList.cc
, MultiConstraint.cc
, DistanceChainbreakEnergy.cc
, ResolutionSwitcher.cc
, StrandConstraints.cc
, ResidualDipolarCouplingEnergy.cc
, Template.cc
, TemplateJumpSetup.cc
, NamedAtomPairConstraint.cc
, ResidualDipolarCouplingEnergyRigidSegments.cc
, AtomTreeDiffJobInputter.cc
, VarianceStatisticsArchive.cc
, NormalizedEvaluatedArchive.cc
, MPIArchiveJobDistributor.cc
, EvaluatedArchive.cc
, ArchiveManager.cc
, ArchiveBase.cc
, FragmentScoreManager.cc
, ResidueVicinityRCG.cc
, InvrotTreeRCG.cc
, InverseRotamersRCG.cc
, ConstraintFileRCG.cc
, NcontactsCalculator.cc
, SheetTopologyFilter.cc
, SecondaryStructureFilter.cc
, NcontactsFilter.cc
, InterlockingAromaFilter.cc
, FragQualFilter.cc
, CoreDunbrackFilter.cc
, DatabaseJobOutputter.cc
, DatabaseJobInputter.cc
, util.cc
, AlignEvaluator.cc
, DesignVsNativeComparison.cc
, TemperedDocking.cc
, DockSetupMover.cc
, MaxSeqSepConstraintSet.cc
, ConstraintEvaluatorCreator.cc
, ConstraintEvaluator.cc
, CombinedConstraintEvaluatorCreator.cc
, CombinedConstraintEvaluator.cc
, RangeFilter.cc
, IgnoreSubsetConstraintSet.cc
, GenericJobInputter.cc
, cm_main.cc
, AlignRmsdTargetEvaluatorCreator.cc
, AlignmentClustering.cc
, Align_RotamerEvaluator.cc
, Align_RmsdEvaluator.cc
, TrialCounterObserver.cc
, TrajectoryRecorder.cc
, TemperingBase.cc
, TemperatureController.cc
, SimulatedTempering.cc
, SilentTrajectoryRecorder.cc
, SidechainMetropolisHastingsMover.cc
, ParallelTempering.cc
, PeakFileFormat_Sparky.cc
, Templates.cc
, HamiltonianExchange.cc
, MinScoreScoreFunction.cc
, MPIHPool_ConvergenceCheck.cc
, Pool_ConvergenceCheck.cc
, CarbonHBondEnergy.cc
, DipolarCoupling.cc
, ResidualDipolarCoupling.cc
, MultiTemperatureTrialCounter.cc
, ResidualDipolarCoupling_Rohl.cc
, DNABFormPotential.cc
, RNA_AtomVDW.cc
, RNA_FullAtomStackingEnergy.cc
, ChemicalShiftAnisotropy.cc
, DNAChiEnergy.cc
, RNA_LowResolutionPotential.cc
, IterativeCentroid.cc
, IterativeBase.cc
, IterativeAbrelax.cc
, HedgeArchive.cc
, FragmentSampler.cc
, FoldConstraints.cc
, DoubleLayerKinematicAbinitio.cc
, ConstraintFragmentSampler.cc
, ClassicAbinitio.cc
, BrokerMain.cc
, AbrelaxMover.cc
, AbrelaxApplication.cc
, SurfaceEnergies.cc
, ScoreFunctionFactory.cc
, ScoreFunction.cc
, BindingSiteConstraint.cc
, RNA_Mg_Energy.cc
, DNATorsionPotential.cc
, RNA_Mg_KnowledgeBasedPotential.cc
, RNA_TorsionPotential.cc
, SecondaryStructure.cc
, AmbiguousNMRDistanceConstraint.cc
, DockingScoreFunction.cc
, RNA_VDW_Energy.cc
, Dssp.cc
, AtomPairConstraint.cc
, PairingsList.cc
, StrandPairing.cc
, NamedAtomID.cc
, BoundConstraint.cc
, Energies.cc
, ContextIndependentGeometricSolEnergy.cc
, ConstraintIO.cc
, GeometricSolEnergy.cc
, OccludedHbondSolEnergy.cc
- TR_BGEDGE()
: SurfaceInteractionGraph.hh
- TR_BGNODE()
: SurfaceInteractionGraph.hh
- tr_control()
: PseudocontactShiftEnergyController.cc
- TR_debug()
: PlaceStubMover.cc
- TR_DS()
: RotamerDots.cc
- TR_EDGE()
: SurfaceInteractionGraph.hh
- TR_energies()
: GenericMonteCarloMover.cc
- tr_labels()
: CrossPeak.cc
- TR_loop()
: CcdLoopClosureMover.cc
- TR_NODE()
: SurfaceInteractionGraph.hh
- TR_PcsEnergyController()
: PcsEnergyController.cc
- TR_PcsGridSearchParameter()
: PcsGridSearchParameter.cc
- TR_PcsGridSearchParameterManager()
: PcsGridSearchParameterManager.cc
- TR_RD()
: RotamerDots.cc
- TR_RDC()
: RotamerDots.cc
- TR_RDRD()
: RotamerDots.cc
- TR_SIG()
: SurfaceInteractionGraph.hh
- TR_SR()
: StructureRestrictor.cc
- TR_STATS()
: SurfaceInteractionGraph.hh
- trans()
: DockingInitialPerturbation.cc
, SymDockingInitialPerturbation.cc
- TRb()
: RBSegmentRelax_main.cc
- TRC()
: CloseOneCDRLoop.cc
- TRG()
: GraftOneCDRLoop.cc
- TRhbonds()
: InterfaceAnalyzerMover.cc
- TRinterface()
: InterfaceAnalyzerMover.cc
- TRO()
: GraftMover.cc
1.8.4
