Here is a list of all file members with links to the files they belong to:

- t -

• T_design() : AnchorMovers.cc
• T_perturb() : AnchorMovers.cc
• T_refine() : AnchorMovers.cc
• T_shared() : AnchorMovers.cc
• TAG_NUM_FORMAT_LENGTH : JobDistributors.hh
• TC() : InterchainPotential.cc
• TorsionList : PhosphateMover.cc
• tr : SecondaryStructureHasResidueFilter.cc , ConstraintPreparer.cc , IterativeCentroid.cc , AlignmentClustering.cc , SheetBuilder.cc
• TR() : PackStatMover.cc , EnsembleEnergy.cc , CloseFold.cc , Anchor.cc , DefineMovableLoops.cc , GrowPeptides.cc
• tr() : WidthFirstSlidingWindowLoopClosure.cc
• TR() : AnchorMoversData.cc , SeededAbinitio_util.cc , SeedFoldTree.cc , Ab_TemplateInfo.cc , SwapSegment.cc , loophash_util.cc
• tr() : AlignRmsdTargetEvaluatorCreator.cc , loopfinder.cc
• TR() : AntibodyFeatures.cc , read_biounit.cc , DdGScan.cc , AntibodyInfo.cc , SaveResfileToDiskFilter.cc , TaskAwareSASAFilter.cc
• tr() : MoverContainer.cc
• TR() : AntibodyModelerProtocol.cc , DatabaseEntryWorkUnit.cc , UnfoldedStateEnergyCalculatorUtil.cc , UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc , UnfoldedStateEnergyCalculatorJobDistributor.cc , MembraneTopologyClaimer.cc , ThreadSequenceOperation.cc , StoreTaskMover.cc , StoreCompoundTaskMover.cc , StoreCombinedStoredTasksMover.cc , SelectResiduesWithinChain.cc , SelectBySASAOperation.cc , SelectByDensityFitOperation.cc , SelectByDeltaScoreOperation.cc , RetrieveStoredTaskOperation.cc , RestrictToTerminiOperation.cc , RestrictToNeighborhoodOperation.cc , RestrictToInterfaceVectorOperation.cc , RestrictToInterfaceOperation.cc , RestrictToAlignedSegments.cc , RestrictResiduesToRepackingOperation.cc , RestrictNonSurfaceToRepackingOperation.cc , RestrictNativeResiduesOperation.cc , RestrictInterGroupVectorOperation.cc , RestrictIdentitiesOperation.cc , RestrictIdentitiesAtAlignedPositions.cc , RestrictChainToRepackingOperation.cc , RestrictByCalculatorsOperation.cc , ProteinInterfaceDesignOperation.cc , ProteinCoreResFilter.cc , PreventResiduesFromRepackingOperation.cc , PreventChainFromRepackingOperation.cc , LinkResidues.cc , JointSequenceOperation.cc , DsspDesignOperation.cc , AddChainMover.cc , AddConstraintsToCurrentConformationMover.cc , CrystalContactsOperation.cc , AlignedThreadOperation.cc , SelectResiduesByLayer.cc , util.cc , SemiExplicitWaterUnsatisfiedPolarsCalculator.cc , SaltBridgeCalculator.cc , PiPiCalculator.cc , PackstatCalculator.cc , NonlocalContactsCalculator.cc , NeighborsByDistanceCalculator.cc , NeighborhoodByDistanceCalculator.cc , InterGroupNeighborsCalculator.cc , FragQualCalculator.cc , CatPiCalculator.cc , BuriedUnsatisfiedPolarsCalculator.cc , NetworkAlgorithms.cc , KCluster.cc , AllowInsert.cc , SymSidechainMinMover.cc , SymDockingLowRes.cc , SymDockingHiRes.cc , SurfaceParameters.cc , SurfaceOrientMover.cc , SurfaceDockingProtocol.cc , FullatomRelaxMover.cc , CentroidRelaxMover.cc , StepWiseSampleAndScreen.cc , FullModelInfoSetupFromCommandLine.cc , VDW_BinScreener.cc , util.cc , TagDefinition.cc , SugarInstantiator.cc , StubDistanceScreener.cc , StubApplier.cc , StepWiseScreener.cc , StepWiseResiduePairScreener.cc , Scorer.cc , SampleApplier.cc , RNA_ChainClosureScreener.cc , RNA_ChainClosableGeometryStubBasedScreener.cc , RNA_ChainClosableGeometryScreener.cc , RNA_ChainClosableGeometryResidueBasedScreener.cc , ResidueContactScreener.cc , ProteinCCD_ClosureScreener.cc , PoseSelectionScreener.cc , PhosphateScreener.cc , PartitionContactScreener.cc , PackScreener.cc , O2PrimeScreener.cc , NativeRMSD_Screener.cc , IntegrationTestBreaker.cc , FastForwardToNextRigidBody.cc , FastForwardToNextResidueAlternative.cc , CentroidDistanceScreener.cc , BulgeApplier.cc , BaseCentroidScreener.cc , BaseBinMapUpdater.cc , AnchorSugarScreener.cc , StepWiseSamplerSizedComb.cc , StepWiseSamplerSizedAny.cc , StepWiseSamplerSized.cc , StepWiseSamplerOneValue.cc , StepWiseSamplerOneTorsion.cc , StepWiseSamplerComb.cc , StepWiseSamplerAny.cc , util.cc , RNA_SuiteStepWiseSampler.cc , RNA_SugarStepWiseSampler.cc , RNA_NucleosideStepWiseSampler.cc , RNA_MC_Suite.cc , RNA_MC_Sugar.cc , RNA_MC_MultiSuite.cc , RNA_KinematicCloser.cc , RNA_KIC_Sampler.cc , RNA_ChiStepWiseSampler.cc , RigidBodyStepWiseSamplerWithResidueList.cc , RigidBodyStepWiseSamplerWithResidueAlternatives.cc , RigidBodyStepWiseSamplerValueRange.cc , RigidBodyStepWiseSampler.cc , EulerAngles.cc , util.cc , ProteinMainChainStepWiseSampler.cc , ProteinFragmentStepWiseSampler.cc , ProteinBetaAntiParallelStepWiseSampler.cc , NoOpStepWiseSampler.cc , MC_OneTorsion.cc , MC_Comb.cc , JumpStepWiseSampler.cc , InputStreamStepWiseSampler.cc , ResidueListStepWiseSampler.cc , ResidueAlternativeStepWiseSamplerComb.cc , ResidueAlternativeStepWiseSampler.cc , ResidueAlternativeSet.cc , CopyDofStepWiseSampler.cc , StepWiseBasicOptions.cc , util.cc , SWA_MoveSelector.cc , StepWiseMonteCarlo.cc , RNA_TorsionMover.cc , RNA_O2PrimeMover.cc , RNA_AddDeleteMonteCarlo.cc , StepWiseMonteCarloOptions.cc , TransientCutpointHandler.cc , ResampleMover.cc , FromScratchMover.cc , DeleteMover.cc , AddOrDeleteMover.cc , AddMover.cc , util.cc , StepWiseWorkingParameters.cc , StepWiseBasicWorkingParameters.cc , util.cc , StepWiseModeler.cc , StepWiseMinimizer.cc , StepWiseConnectionSampler.cc , scoring_util.cc , util.cc , SugarVirtualizeMover.cc , SugarModeling.cc , SugarInstantiateMover.cc , StepWiseRNA_VirtualSugarSamplerFromStringList.cc , StepWiseRNA_VirtualSugarSampler.cc , StepWiseRNA_VirtualSugarJustInTimeInstantiator.cc , StepWiseRNA_ResidueInfo.cc , StepWiseRNA_OutputData.cc , StepWiseRNA_CombineLongLoopFilterer.cc , CDRsMinPackMin.cc , util.cc , PhosphateMover.cc , PhosphateMove.cc , MultiPhosphateSampler.cc , O2PrimePacker.cc , RNA_HelixAssembler.cc , RNA_VDW_BinChecker.cc , RNA_ChainClosureChecker.cc , RNA_ChainClosableGeometryChecker.cc , RNA_BaseCentroidChecker.cc , RNA_AtrRepChecker.cc , util.cc , BulgeUnApplyMover.cc , BulgeApplyMover.cc , StepWiseProteinBackboneSampler.cc , util.cc , StepWiseProteinKIC_LoopBridger.cc , StepWiseProteinCCD_MultiPoseCloser.cc , StepWiseProteinCCD_Closer.cc , InputStreamWithResidueInfo.cc , ProteinAtrRepChecker.cc , util.cc , PolarHydrogenPacker.cc , util.cc , StepWisePacker.cc , StepWiseMasterPacker.cc , SideChainCopier.cc , output_util.cc , StepWiseRNA_ModelerOptions.cc , StepWiseProteinModelerOptions.cc , StepWiseModelerOptions.cc , StepWiseBasicModelerOptions.cc , util.cc , file_util.cc , constraint_util.cc , util.cc , StepWisePoseAligner.cc , StepWiseLegacyClustererSilentBased.cc , StepWiseLegacyClusterer.cc , StepWiseClusterer.cc , SimpleRMSD_Screener.cc , SimplePoseSelection.cc , RNA_AtrRepScreener.cc , ProteinAtrRepScreener.cc , util.cc , StepWiseRNA_WorkingParametersSetup.cc , StepWiseRNA_PoseSetupFromCommandLine.cc , StepWiseRNA_PoseSetup.cc , StepWiseRNA_PoseSelection.cc , StepWiseRNA_Minimizer.cc , StepWiseRNA_Clusterer.cc , RNA_AnalyticLoopCloser.cc , util.cc , StepWiseProteinPoseSetup.cc , StepWiseProteinMinimizer.cc , WobbleMover.cc , UniformPositionMover.cc , Tumble.cc , TorsionSetMover.cc , TorsionDOFMover.cc , TaskAwareMinMover.cc , TailsScoreMover.cc , TaskAwareSymMinMover.cc , SymPackRotamersMover.cc , SymMinMover.cc , SymDockingInitialPerturbation.cc , SwitchResidueTypeSetMover.cc , SwitchChainOrderMover.cc , SidechainMover.cc , SidechainMCMover.cc , PerturbRotamerSidechainMover.cc , PerturbChiSidechainMover.cc , ShortBackrubMover.cc , SetReturningPackRotamersMover.cc , SequenceProfileMover.cc , RotamerTrialsMover.cc , RotamerTrialsMinMover.cc , RingConformationMover.cc , ReturnSidechainMover.cc , ResidueTypeConstraintMover.cc , ResetBaselineMover.cc , ReportEffectivePKA.cc , RandomTorsionMover.cc , RandomOmegaFlipMover.cc , PSSM2BfactorMover.cc , PeptideStapleMover.cc , OopRandomSmallMover.cc , OopRandomPuckMover.cc , OopPuckMover.cc , OopPatcher.cc , OopMover.cc , MonteCarloTest.cc , MonteCarloReset.cc , MonteCarloRecover.cc , MakePolyXMover.cc , LoadUnboundRotMover.cc , LoadPDBMover.cc , HbsPatcher.cc , GenericMonteCarloMover.cc , DME_FilterMover.cc , DesignRepackMover.cc , CoupledMover.cc , CopyDofMover.cc , ContingentAcceptMover.cc , ConstraintSetMover.cc , ConstrainToIdealMover.cc , ConsensusDesignMover.cc , ChiralMover.cc , ChangeAndResetFoldTreeMover.cc , BoltzmannRotamerMover.cc , AlignChainMover.cc , BackboneMover.cc
• tr() : IterativeFullatom.cc , cm_main.cc , TrialCounter.cc
• TR() : CDRClusterMatcher.cc , BBConRotMover.cc , BBGaussianMover.cc , ParatopeEpitopeSiteConstraintMover.cc
• tr() : CrossPeak.cc
• TR() : ParatopeSiteConstraintMover.cc , AntibodyDatabaseManager.cc
• tr() : GenericJobInputter.cc , CrossPeakInfo.cc
• TR() : CDRSetOptionsParser.cc , AntibodyDesignModeler.cc
• tr() : CrossPeakList.cc
• TR() : AntibodyDesignMover.cc , Interface.cc , sasapack.cc , util.cc , SavePoseMover.cc , PoseSelector.cc , PosePropertyReporter.cc , RotateJumpAxisMover.cc , RollMover.cc , RB_geometry.cc , util.cc , RelaxProtocolBase.cc , Ramady.cc , MiniRelax.cc , FastRelax.cc , ClassicRelax.cc , CentroidRelax.cc , AtomCoordinateCstMover.cc , util.cc , ReportPSSMDifference.cc , read_patchdock.cc , ParserJobInputter.cc , SubroutineMover.cc , PlaceUtils.cc , PlaceStubMover.cc , PlaceSimultaneouslyMover.cc , PlacementMinimizationMover.cc , PlacementAuctionMover.cc , InterfaceRecapitulationMover.cc , design_utils.cc , ClusterPoseSelector.cc , BasicPoseSelectors.cc , BasicPosePropertyReporters.cc , MultistateFitnessFunction.cc , PNatLigPoseOptEData.cc , NormalModeRelaxMover.cc , NormalModeMultiFunc.cc , NormalMode.cc , OopDockDesignProtocol.cc , OopCreatorMover.cc , NcbbDockDesignProtocol.cc , MultiStatePacker.cc , SimulatedTempering.cc , ReplicaExchangeMC.cc , MoverStatistics.cc , MoverForPoseList.cc , MonteCarlo.cc , FilterMover.cc , DualMonteCarlo.cc , DsspMover.cc , ZincSiteFinder.cc , ZincHeterodimerMover.cc , MatchGrafter.cc , AddZincSiteConstraints.cc , VisualizeMembraneMover.cc , VisualizeEmbeddingMover.cc , SymmetricAddMembraneMover.cc , SetMembranePositionMover.cc , RandomMembranePositionMover.cc , MembranePositionFromTopologyMover.cc , SpanFileLoader.cc , util.cc , EmbeddingDef.cc , Embedding.cc , AntibodyDesignMoverGenerator.cc , SymDofMoverSampler.cc , SymDofMover.cc , OligomericAverageDegreeFilter.cc , GetRBDOFValues.cc , ExtractSubposeMover.cc , ClashCheckFilter.cc , BuildingBlockInterfaceOperation.cc , MatchScoreWriter.cc , util.cc , loopfinder.cc , SmallMinCCDTrial.cc , ShearMinCCDTrial.cc , RepackTrial.cc , LoopRefineInnerCycleContainer.cc , LoopRefineInnerCycle.cc , KinematicWrapper.cc , KinematicMover.cc , CCDLoopClosureMover.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 , util.cc , InsertChunkMover.cc , HybridizeSetup.cc , HybridizeProtocol.cc , HybridizeFoldtreeDynamic.cc , FoldTreeHybridize.cc , DomainAssembly.cc , ChunkTrialMover.cc , BackboneTorsionSampler.cc , BackboneTorsionPerturbation.cc , FitSimpleHelixMultiFunc.cc , util.cc , KeepRegionMover.cc , GraftMoverBase.cc , CCDEndsGraftMover.cc , AnchoredGraftMover.cc , VallData.cc , VallProvider.cc , RemodelConstraintGenerator.cc , RemoveCsts.cc , NtoC_RCG.cc , utility.cc , LayerDesignOperation.cc , InterlockAroma.cc , FlxbbDesign.cc , DesignAroundOperation.cc , DesignTask.cc , FloppyTailMover.cc , FlexPepDockingProtocol.cc , FlexPepDockingPoseMetrics.cc , FlexPepDockingLowRes.cc , FlexPepDockingFlags.cc , FlexPepDockingAbInitio.cc , util.cc , StrandPairing.cc , Sheet.cc , HSSTriplet.cc , HelixPairing.cc , BetaAlphaBetaMotif.cc , SheetConstraintsRCG.cc , SSPairPotential.cc , NatbiasStrandPairPotential.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 , WaterFeatures.cc , StructureFeatures.cc , ProtocolFeatures.cc , InterfaceFeatures.cc , HelixBundleFeatures.cc , util.cc , RNA_Relaxer.cc , RNA_Minimizer.cc , RNA_LoopCloser.cc , RNA_FragmentMover.cc , RNA_ChunkLibrary.cc , BasePairStepLibrary.cc , RemoveLigandFilter.cc , EnzRepackMinimize.cc , EnzFilters.cc , EnzdesJobInputter.cc , util.cc , ScaleMapIntensities.cc , ReportFSC.cc , DensityMorphingMover.cc , BfactorFittingMover.cc , util.cc , SidechainMinMover.cc , metrics.cc , MPDockingMover.cc , EllipsoidalRandomizationMover.cc , DockTaskFactory.cc , DockMCMProtocol.cc , DockMCMCycle.cc , DockingProtocol.cc , DockingPrepackProtocol.cc , DockingLowResEnsemble.cc , DockingLowRes.cc , DockingInitialPerturbation.cc , DockingHighResLegacy.cc , util.cc , DockingEnsemblePrepackProtocol.cc , DockingEnsemble.cc , DockFilters.cc , ConformerSwitchMover.cc , RotamerDNAHBondFilter.cc , ExposedHydrophobicsFilter.cc , ddGMover.cc , ddG_main.cc , PeptideStubMover.cc , DeclareBond.cc , CreateTorsionConstraint.cc , CreateDistanceConstraint.cc , CreateAngleConstraint.cc , CoarseRNA_LoopCloser.cc , CoarseRNA_Fragments.cc , APCluster.cc , pool_util.cc , HPool.cc , BranchAngleOptimizer.cc , BackrubSidechainMover.cc , BackrubMover.cc , Ubiquitin_E2C_Modeler.cc , LHSnugFitLegacy.cc , LHRepulsiveRampLegacy.cc , GraftMover.cc , CDRH3Modeler.cc , AntibodyModeler.cc , AntibodyClass.cc , util.cc , SnugDockProtocol.cc , SnugDock.cc , RefineOneCDRLoopCentroid.cc , RefineOneCDRLoop.cc , RefineBetaBarrel.cc , ModelCDRH3.cc , metrics.cc , LHRepulsiveRamp.cc , H3RefineCCD.cc , H3PerturbCCD.cc , H3CterInsert.cc , GraftCDRLoopsProtocol.cc , ResidueProbDesignOperation.cc , ConservativeDesignOperation.cc , CDRSeqDesignOptions.cc , CDRGraftDesignOptions.cc , AntibodySeqDesignTFCreator.cc
• tr() : FragmentCM.cc , KinematicAbinitio.cc , IgnoreSubsetConstraintSet.cc , DistanceScoreMover.cc
• TR() : AntibodyGraftDesignMover.cc , AntibodySeqDesignMover.cc
• tr() : FloatingResonance.cc , BindingSiteConstraint.cc , FragsToAtomDist.cc , LabelResonance.cc , KinematicControl.cc , CombinedConstraintEvaluator.cc , MethylNames.cc , NoesyModule.cc , CombinedConstraintEvaluatorCreator.cc , PeakAssignment.cc , PeakAssignmentResidueMap.cc , InterRepeatContactFilter.cc
• TR() : LoopAnalyzerMover.cc , InterfaceAnalyzerMover.cc , util.cc , MPSymDockMover.cc , StepWiseMonteCarloJobDistributor.cc , StepWiseCSA_JobDistributor.cc , PrecomputedLibraryMover.cc , RepeatPropagationMover.hh , MPFastRelaxMover.cc , util.cc , TranslationRotationMover.cc , TransformIntoMembraneMover.cc , util.cc , FlipMover.cc , SchemePlaceMotifsMover.cc , util.cc , MPDockingSetupMover.cc , util.cc
• tr() : util.cc , TopologyClaimerFactory.cc , TopologyClaimer.cc , TopologyBroker.cc , TMHTopologySamplerClaimer.cc , TemplateJumpClaimer.cc , TemplateFragmentClaimer.cc , SymmetryClaimer.cc , StartStructClaimer.cc , SequenceNumberResolver.cc , SequenceClaimer.cc , RigidChunkClaimer.cc
• TR() : AddMembraneMover.cc
• tr() : LoopFragmentClaimer.cc , FragmentJumpClaimer.cc , FragmentClaimer.cc , FoldandDockClaimer.cc , FibrilModelingClaimer.cc , DisulfJumpClaimer.cc , DensityScoringClaimer.cc , CutBiasClaimer.cc , CoordConstraintClaimer.cc , ConstraintEvaluatorWrapperCreator.cc , ConstraintEvaluatorWrapper.cc , ConstraintClaimer.cc , DofClaim.cc , BasicJumpClaimer.cc , AsymFoldandDockClaimer.cc , SeqprofConsensusOperation.cc , InteractingRotamerExplosion.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 , ExtendedPoseMover.cc , StructureSimilarityEvaluatorCreator.cc
• TR() : DatabaseThread.cc
• tr() : 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 , RangeFilter.cc , 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
• TR() : DockingHighRes.cc
• tr() : CamShiftEvaluatorCreator.cc , CamShiftEvaluator.cc , AbinitioBaseFilter.cc , ResidualDipolarCouplingRigidSegments.cc , ResidualDipolarCouplingEnergyRigidSegments.cc , relax_main.cc , cst_util.cc , StructureIndependentPeakCalibrator.cc , StructureDependentPeakCalibrator.cc , ResonanceList.cc , Resonance.cc , ProtonResonance.cc , PeakFileFormat_xpk.cc , PeakFileFormat_Sparky.cc , FragmentJumpCM.cc , KinematicTaskControl.cc , COMCoordinateConstraint.cc , PeakCalibrator.cc , PeakFileFormat.cc , ConstraintEvaluator.cc , LoopJumpFoldCst.cc , ConstraintEvaluatorCreator.cc , MaxSeqSepConstraintSet.cc , JumpSampleData.cc , MembraneAbinitio.cc , DockSetupMover.cc , TemperedDocking.cc , PairingStatistics.cc , AutoCutData.cc , CutBiasClaim.cc , IntraRepeatContactFilter.cc , RigidChunkCM.cc , SameStrand.cc , RandomSheetBuilder.cc , PairingLibrary.cc , DisulfPairingsList.cc , DisulfPairingLibrary.cc , SilentFileJobOutputter.cc , SilentFileJobInputter.cc , PoseInputStreamJobInputter.cc , MPIMultiCommJobDistributor.cc , MPIFileBufJobDistributor.cc , LazySilentFileJobInputter.cc , BatchJobInputter.cc , AtomTreeDiffJobInputter.cc , VarianceStatisticsArchive.cc , NormalizedEvaluatedArchive.cc , MetalloClaimer.cc , EvaluatedArchive.cc , ArchiveManager.cc , ArchiveBase.cc , FragmentScoreManager.cc , ResidueVicinityRCG.cc , InvrotTreeRCG.cc , InverseRotamersRCG.cc , ConstraintFileRCG.cc , NcontactsCalculator.cc , SheetTopologyFilter.cc , SecondaryStructureFilter.cc , SecondaryStructureCountFilter.cc , NcontactsFilter.cc , InterlockingAromaFilter.cc , FragQualFilter.cc
• TR() : FilterStructs.cc
• tr() : DatabaseJobOutputter.cc , DatabaseJobInputter.cc , util.cc , AlignEvaluator.cc , DesignVsNativeComparison.cc , ProtectedConformation.cc , EnvMover.cc , Environment.cc , EnvClaimBroker.cc , DofUnlock.cc , ClientMover.cc , XYZClaim.cc , VirtResClaim.cc , TorsionClaim.cc , Protocol.cc , EnvClaim.cc , ChiWellRmsdEvaluator.cc , JumpClaim.cc , ResolutionSwitcher.cc , StagePreparer.cc , StrandConstraints.cc , Template.cc , AbrelaxApplication.cc , StructPerturberCM.cc , TemplateJumpSetup.cc , Templates.cc , BrokerMain.cc , AsyncMPITemperingBase.cc , BiasedMonteCarlo.cc , AbrelaxMover.cc , ClassicAbinitio.cc , BiasEnergy.cc , Align_RotamerEvaluator.cc , Align_RmsdEvaluator.cc , TrialCounterObserver.cc , TrajectoryRecorder.cc , TemperingBase.cc , TemperatureController.cc , SimulatedTempering.cc , MPIArchiveJobDistributor.cc , SidechainMetropolisHastingsMover.cc , ParallelTempering.cc , MultiTemperatureTrialCounter.cc , MetropolisHastingsMover.cc , Pool_ConvergenceCheck.cc , MPIHPool_ConvergenceCheck.cc , CoreDunbrackFilter.cc , SheetFilter.cc , HamiltonianExchange.cc , ConstraintFragmentSampler.cc , AbscriptLoopCloserCM.cc , DoubleLayerKinematicAbinitio.cc , FoldConstraints.cc , AbscriptMover.cc , FragmentSampler.cc , SilentTrajectoryRecorder.cc , HedgeArchive.cc , AbscriptStageMover.cc , IterativeAbrelax.cc , IterativeBase.cc
• tr_control() : PseudocontactShiftEnergyController.cc , PseudocontactShiftEnergyController_Ts1.cc , PseudocontactShiftEnergyController_Ts2.cc , PseudocontactShiftEnergyController_Ts4.cc , PseudocontactShiftEnergyController_Ts3.cc
• TR_debug() : PlaceStubMover.cc
• TR_energies() : GenericMonteCarloMover.cc
• tr_labels() : ResonanceList.cc , CrossPeakInfo.cc
• TR_PcsEnergyController() : PcsEnergyController.cc
• TR_PcsGridSearchParameter() : PcsGridSearchParameter.cc
• TR_PcsGridSearchParameterManager() : PcsGridSearchParameterManager.cc
• TR_PYMOL() : AddZincSiteConstraints.cc
• TR_REMODEL() : RemodelData.cc
• TR_SR() : StructureRestrictor.cc
• trans() : SymDockingInitialPerturbation.cc , DockingInitialPerturbation.cc
• TRb() : RBSegmentRelax_main.cc
• TRC() : CloseOneCDRLoop.cc
• TRDEBUG : MPI_WorkUnitManager.cc , MPI_WorkUnitManager_Slave.cc , MPI_Refine_Master.cc , MPI_LoopHashRefine_Master.cc , MPI_LoopHashRefine_Emperor.cc , MPI_Refine_Emperor.cc , MPI_LoopHashRefine.cc , MPI_Refinement.cc
• TRG() : GraftedStemOptimizer.cc , GraftOneCDRLoop.cc
• TRhbonds() : InterfaceAnalyzerMover.cc
• TRinterface() : InterfaceAnalyzerMover.cc
• TRO() : GraftMover.cc
• TYPE_NAME() : AutoCutData.cc , JumpSampleData.cc