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
- THROW_EXCEPTION
: serialize_pose.cc
- torsion_info
: util.cc
- TorsionList
: PhosphateMover.cc
- TR()
: ring_conformer_io.cc
, PsiPredInterface.cc
, BasePair.cc
, PoissonBoltzmannEnergy.cc
, SSPredictionFilter.cc
, sasapack.cc
- tr()
: PeakCalibrator.cc
, PeakFileFormat.cc
- TR()
: InterchainPotential.cc
- tr()
: PeakFileFormat_Sparky.cc
, PeakFileFormat_xpk.cc
- TR()
: DisulfidizeMover.cc
, Interface.cc
- tr()
: ProtonResonance.cc
, Resonance.cc
- TR()
: EnsembleEnergy.cc
- tr()
: ResonanceList.cc
, StructureDependentPeakCalibrator.cc
- TR()
: UnfoldedStateEnergy.cc
, ConsensusLoopDesign.cc
, CloseFold.cc
- tr()
: StructureIndependentPeakCalibrator.cc
, cst_util.cc
- TR()
: DefineMovableLoops.cc
- tr()
: relax_main.cc
, ResidualDipolarCouplingEnergyRigidSegments.cc
- TR()
: util.cc
, GrowPeptides.cc
- tr()
: ResidualDipolarCouplingRigidSegments.cc
, AbinitioBaseFilter.cc
- TR()
: SeededAbinitio_util.cc
- tr()
: CamShiftEvaluator.cc
, CamShiftEvaluatorCreator.cc
- TR()
: BaseStack.cc
, VdWTinkerEnergy.cc
, RotamerDNAHBondFilter.cc
, SeedFoldTree.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
, MetalloClaimer.cc
, 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
, SSElementMotifContactFilter.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
, RangeFilter.cc
, PredictedBurialFnEvaluatorCreator.cc
, PoolEvaluatorCreator.cc
, PDDFScoreFilter.cc
, PalesEvaluatorCreator.cc
, PalesEvaluator.cc
, PackStatFilter.cc
, PackerNeighborGraphFilter.cc
, NativeEvaluatorCreator.cc
, LeastNativeLike9merFilter.cc
, JumpNrEvaluatorCreator.cc
, JScoreEvaluatorCreator.cc
, IntraRepeatContactFilter.cc
, InterRepeatContactFilter.cc
, HolesFilter.cc
, ExtraScoreEvaluatorCreator.cc
, ExternalEvaluator.cc
, ChiWellRmsdEvaluator.cc
, ChiWellRmsdEvaluatorCreator.cc
- TR()
: SwapSegment.cc
- tr()
: COFilter.cc
, ConservedPosMutationFilter.cc
- TR()
: ConformerSwitchMover.cc
, loophash_util.cc
- tr()
: ConstraintScoreCutoffFilter.cc
, ContactMapEvaluatorCreator.cc
- TR()
: read_biounit.cc
, MMBondAngleResidueTypeParam.cc
, DockFilters.cc
, DdGScan.cc
, SaveResfileToDiskFilter.cc
, DockingEnsemble.cc
, TaskAwareSASAFilter.cc
, A3BHbsMover.cc
, cif_reader.cc
, leontis_westhof_util.cc
, MultipoleElecPotential.cc
, DockingEnsemblePrepackProtocol.cc
, A3BHbsPatcher.cc
- tr()
: PeakAssignmentResidueMap.cc
, PeakAssignment.cc
, NoesyModule.cc
, MethylNames.cc
, LabelResonance.cc
, FragsToAtomDist.cc
, FloatingResonance.cc
, DistanceScoreMover.cc
, CrossPeakList.cc
, CrossPeakInfo.cc
, CrossPeak.cc
, TrialCounter.cc
, loopfinder.cc
, WidthFirstSlidingWindowLoopClosure.cc
, SheetBuilder.cc
, SameStrand.cc
, RandomSheetBuilder.cc
, PairingLibrary.cc
, DisulfPairingsList.cc
, DisulfPairingLibrary.cc
, SilentFileJobOutputter.cc
, SilentFileJobInputter.cc
, PoseInputStreamJobInputter.cc
, MPIMultiCommJobDistributor.cc
, MPIFileBufJobDistributor.cc
, LazySilentFileJobInputter.cc
, LargeNstructJobInputter.cc
, BatchJobInputter.cc
, AtomTreeDiffJobInputter.cc
, VarianceStatisticsArchive.cc
, NormalizedEvaluatedArchive.cc
, MPIArchiveJobDistributor.cc
, EvaluatedArchive.cc
, ArchiveManager.cc
, ArchiveBase.cc
, FragmentScoreManager.cc
, ResidueVicinityRCG.cc
, InvrotTreeRCG.cc
, InverseRotamersRCG.cc
, NcontactsCalculator.cc
, SheetTopologyFilter.cc
, SecondaryStructureHasResidueFilter.cc
, SecondaryStructureFilter.cc
, SecondaryStructureCountFilter.cc
, NcontactsFilter.cc
, InterlockingAromaFilter.cc
, FragQualFilter.cc
, CoreDunbrackFilter.cc
, DatabaseJobOutputter.cc
, DatabaseJobInputter.cc
, util.cc
, AlignEvaluator.cc
, DesignVsNativeComparison.cc
, ProtectedConformation.cc
, EnvMover.cc
, Environment.cc
, EnvExcn.cc
, EnvClaimBroker.cc
, DofUnlock.cc
, ClientMover.cc
, XYZClaim.cc
, VirtResClaim.cc
, TorsionClaim.cc
, JumpClaim.cc
, EnvClaim.cc
, CutBiasClaim.cc
, AutoCutData.cc
, TemperedDocking.cc
, DockSetupMover.cc
, MaxSeqSepConstraintSet.cc
, ConstraintEvaluatorCreator.cc
, ConstraintEvaluator.cc
, COMCoordinateConstraint.cc
, CombinedConstraintEvaluatorCreator.cc
, CombinedConstraintEvaluator.cc
, BindingSiteConstraint.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
, MultiTemperatureTrialCounter.cc
, MetropolisHastingsMover.cc
, Pool_ConvergenceCheck.cc
, MPIHPool_ConvergenceCheck.cc
, HamiltonianExchange.cc
, BiasEnergy.cc
, BiasedMonteCarlo.cc
, AsyncMPITemperingBase.cc
, util.cc
, Templates.cc
, TemplateJumpSetup.cc
, Template.cc
, StrandConstraints.cc
, ResolutionSwitcher.cc
, Protocol.cc
, PairingStatistics.cc
, MembraneAbinitio.cc
, LoopJumpFoldCst.cc
, KinematicTaskControl.cc
, KinematicControl.cc
, KinematicAbinitio.cc
, IterativeFullatom.cc
, IterativeCentroid.cc
, IterativeBase.cc
, IterativeAbrelax.cc
, HedgeArchive.cc
, FragmentSampler.cc
, FoldConstraints.cc
, DoubleLayerKinematicAbinitio.cc
, ConstraintFragmentSampler.cc
, ClassicAbinitio.cc
, BrokerMain.cc
, StructPerturberCM.cc
, StagePreparer.cc
, RigidChunkCM.cc
, JumpSampleData.cc
- TR()
: A3BHbsRandomSmallMover.cc
- tr()
: FragmentCM.cc
, ConstraintPreparer.cc
, AbscriptStageMover.cc
, AbscriptMover.cc
, AbscriptLoopCloserCM.cc
, AbrelaxMover.cc
, AbrelaxApplication.cc
, UnfoldedStatePotential.cc
, SurfaceEnergies.cc
, ScoreFunctionFactory.cc
, ScoreFunction.cc
, StackElecEnergy.cc
, RNA_VDW_Energy.cc
, RNA_LowResolutionPotential.cc
, RNA_AtomVDW.cc
, ResidualDipolarCoupling_Rohl.cc
, ResidualDipolarCoupling.cc
, MinScoreScoreFunction.cc
, ResidualDipolarCouplingEnergy.cc
, DistanceChainbreakEnergy.cc
, DipolarCouplingEnergy.cc
, ContactOrderEnergy.cc
, ChemicalShiftAnisotropyEnergy.cc
, RNA_MgPointEnergy.cc
, MgKnowledgeBasedPotential.cc
, LoopCloseEnergy.cc
, OccludedHbondSolEnergy_onebody.cc
, OccludedHbondSolEnergy.cc
, ContextDependentGeometricSolEnergy.cc
, Energies.cc
, StrandPairing.cc
, PairingsList.cc
, Dssp.cc
, DockingScoreFunction.cc
, DNATorsionPotential.cc
, DNAChiEnergy.cc
, DNABFormPotential.cc
, DipolarCoupling.cc
, NamedAtomPairConstraint.cc
, MultiConstraint.cc
, LocalCoordinateConstraint.cc
, CoordinateConstraint.cc
, ConstraintIO.cc
, BoundConstraint.cc
, AtomPairConstraint.cc
, AmbiguousNMRDistanceConstraint.cc
, ChemicalShiftAnisotropy.cc
, CarbonHBondEnergy.cc
, ResidueCoordinateChangeList.cc
, BinarySilentStruct.cc
, NamedAtomID.cc
, SecondaryStructure.cc
, SequenceAnnotation.cc
, LocalPosition.cc
, FoldTreeSketch.cc
, EnvCore.cc
, DofPassport.cc
- TR()
: 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
, ResidueProbDesignOperation.cc
, ProteinInterfaceDesignOperation.cc
, ProteinCoreResFilter.cc
, PreventResiduesFromRepackingOperation.cc
, PreventChainFromRepackingOperation.cc
, MutationSetDesignOperation.cc
, LinkResidues.cc
, JointSequenceOperation.cc
, DsspDesignOperation.cc
, DesignAroundOperation.cc
, DatabaseThread.cc
, CrystalContactsOperation.cc
, ConservativeDesignOperation.cc
, AlignedThreadOperation.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
, CalcInterNeighborGroup.cc
, AtomLevelDomainMap.cc
, AtomID_Mapper.cc
, SymSidechainMinMover.cc
, SymDockingLowRes.cc
, SymDockingHiRes.cc
, MPSymDockMover.cc
, SurfaceParameters.cc
, SurfaceOrientMover.cc
, SurfaceDockingProtocol.cc
, FullatomRelaxMover.cc
, CentroidRelaxMover.cc
, StepWiseSampleAndScreen.cc
, DockingHighRes.cc
, AddChainMover.cc
, StepWiseCSA_JobDistributor.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
, IntegrationTestBreaker.cc
, FastForwardToNextRigidBody.cc
, FastForwardToNextResidueAlternative.cc
, CentroidDistanceScreener.cc
, BulgeApplier.cc
, BaseCentroidScreener.cc
, BaseBinMapUpdater.cc
, AnchorSugarScreener.cc
, AlignRMSD_Screener.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
, SubMotifLibrary.cc
, StepWiseMonteCarlo.cc
, RNA_TorsionMover.cc
, RNA_O2PrimeMover.cc
, RNA_AddDeleteMonteCarlo.cc
, StepWiseMonteCarloOptions.cc
, VaryLoopLengthMover.cc
, TransientCutpointHandler.cc
, StepWiseMoveSelector.cc
, StepWiseMove.cc
, StepWiseMasterMover.cc
, ResampleMover.cc
, StepWiseMoveSelectorOptions.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
, VirtualSugarSamplerFromStringList.cc
, VirtualSugarSampler.cc
, VirtualSugarJustInTimeInstantiator.cc
, util.cc
, SugarVirtualizeMover.cc
, SugarModeling.cc
, SugarInstantiateMover.cc
, StepWiseRNA_ResidueInfo.cc
, StepWiseRNA_OutputData.cc
, StepWiseRNA_CombineLongLoopFilterer.cc
, util.cc
, PhosphateMover.cc
, PhosphateMove.cc
, MultiPhosphateSampler.cc
, O2PrimePacker.cc
, RNA_HelixAssembler.cc
, VDW_RepScreenInfo.cc
, VDW_Grid.cc
, VDW_CachedRepScreenInfo.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
, AddConstraintsToCurrentConformationMover.cc
, StepWiseProteinCCD_Closer.cc
, InputStreamWithResidueInfo.cc
, ProteinAtrRepChecker.cc
, PrecomputedLibraryMover.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
, TriazolamerRandomSmallMover.cc
, TriazolamerMover.cc
, TorsionSetMover.cc
, TorsionDOFMover.cc
, TaskAwareMinMover.cc
, TailsScoreMover.cc
, TaskAwareSymMinMover.cc
, SymPackRotamersMover.cc
, SymMinMover.cc
, SymDockingInitialPerturbation.cc
, SwitchResidueTypeSetMover.cc
, SwitchChainOrderMover.cc
, StructProfileMover.cc
, SimpleThreadingMover.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
, RepeatPropagationMover.hh
, RandomTorsionMover.cc
, RandomOmegaFlipMover.cc
, PSSM2BfactorMover.cc
, PeriodicBoxMover.cc
, PeptideStapleMover.cc
, OopRandomSmallMover.cc
, OopRandomPuckMover.cc
, OopPuckMover.cc
, OopPatcher.cc
, OopMover.cc
, MonteCarloTest.cc
, MonteCarloReset.cc
, MonteCarloRecover.cc
, MergePDBMover.cc
, MakePolyXMover.cc
, LoadUnboundRotMover.cc
, LoadPDBMover.cc
, HbsPatcher.cc
, GenericMonteCarloMover.cc
, DME_FilterMover.cc
, DesignRepackMover.cc
, DeleteChainsMover.cc
, CoupledMover.cc
, CopyDofMover.cc
, ContingentAcceptMover.cc
, ConstraintSetMover.cc
, ConstrainToIdealMover.cc
, ConsensusDesignMover.cc
, ChiralMover.cc
, ChangeAndResetFoldTreeMover.cc
, BoltzmannRotamerMover.cc
, BBGaussianMover.cc
, BBDihedralSamplerMover.cc
, BBConRotMover.cc
, NVlookup.cc
, DockingHighResLegacy.cc
, AlignChainMover.cc
, BackboneMover.cc
, DockingInitialPerturbation.cc
, SmallBBSampler.cc
, SugarBBSampler.cc
, RNA_BasePairClassifier.cc
, P_AA.cc
, DockingLowRes.cc
, DockingLowResEnsemble.cc
, P_AA_ss.cc
, DockingPrepackProtocol.cc
, DockingProtocol.cc
, RingConformerSet.cc
, cif_writer.cc
, RNA_SuiteName.cc
, compute_holes_score.cc
, DockMCMCycle.cc
, DockMCMProtocol.cc
, SimplePDB.cc
, DockTaskFactory.cc
, EllipsoidalRandomizationMover.cc
, util.cc
, SavePoseMover.cc
, PoseSelector.cc
, PosePropertyReporter.cc
, RotateJumpAxisMover.cc
, RollMover.cc
, RB_geometry.cc
, TaskSelector.cc
, MetapatchEnumeration.cc
, util.cc
, RelaxProtocolBase.cc
, RangeRelaxMover.cc
, Ramady.cc
, MiniRelax.cc
, MPRangeRelaxMover.cc
, MPFastRelaxMover.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
, NearNativeLoopCloser.cc
, InsertResMover.cc
, FixAllLoopsMover.cc
, MultistateFitnessFunction.cc
, PNatLigPoseOptEData.cc
, NormalModeRelaxMover.cc
, NormalModeMultiFunc.cc
, NormalMode.cc
, util.cc
, SecStructMinimizeMultiFunc.cc
, SecStructMinimizeMover.cc
, SecStructFinder.cc
, OopDockDesignProtocol.cc
, OopCreatorMover.cc
, NcbbDockDesignProtocol.cc
, MultiStatePacker.cc
, util.cc
, SimulatedTempering.cc
, ReplicaExchangeMC.cc
, MoverStatistics.cc
, MoverForPoseList.cc
, MoverContainer.cc
, MonteCarlo.cc
, FilterMover.cc
, DualMonteCarlo.cc
, DsspMover.cc
, ConstraintGenerator.cc
, ZincSiteFinder.cc
- tr()
: FragmentJumpCM.cc
- TR()
: MatchGrafter.cc
, AddZincSiteConstraints.cc
, VisualizeMembraneMover.cc
, VisualizeEmbeddingMover.cc
, util.cc
, TranslationRotationMover.cc
, TransformIntoMembraneMover.cc
, TiltMover.cc
, util.cc
, SymmetricAddMembraneMover.cc
, SpinAroundPartnerMover.cc
, SetMembranePositionMover.cc
, RandomMembranePositionMover.cc
, OptimizeProteinEmbeddingMover.cc
, OptimizeMembranePositionMover.cc
, MPQuickRelaxMover.cc
, MPMutateRelaxMover.cc
, MembranePositionFromTopologyMover.cc
, EmbeddingDef.cc
, Embedding.cc
, FlipMover.cc
, SampleTiltAngles.cc
, MakeCanonicalHelix.cc
, AddMPLigandMover.cc
, AddMembraneMover.cc
, SymDofMoverSampler.cc
, SymDofMover.cc
, SchemePlaceMotifsMover.cc
, OligomericAverageDegreeFilter.cc
, GetRBDOFValues.cc
, ExtractSubposeMover.cc
, ClashCheckFilter.cc
, BuildingBlockInterfaceOperation.cc
, MatchScoreWriter.cc
, util.cc
, SampleGrid.cc
, minimize_util.cc
, MgWaterHydrogenPacker.cc
, MgScanner.cc
, MgOrbitalFrameFinder.cc
, MgMonteCarlo.cc
, MgMinimizer.cc
, MgHydrater.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
, util.cc
, ShuffleJobDistributor.cc
, PDBJobOutputter.cc
, PDBJobInputter.cc
, FragSetLoader.cc
, FragmentReader.cc
, util.cc
, MPIWorkPoolJobDistributor.cc
, MPIWorkPartitionJobDistributor.cc
, JobsContainer.cc
, Job.cc
, InnerMultiThreadingJob.cc
, InnerJob.cc
, FileSystemJobDistributor.cc
, FileJobOutputter.cc
, EnsembleJobInputter.cc
, BOINCJobDistributor.cc
, AtomTreeDiffJobOutputter.cc
, util.cc
, WeightedFragmentSmoothTrialMover.cc
, util.cc
, InsertChunkMover.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
, ReduceFragLengthMover.cc
, MergeFragSetMover.cc
, FragSetFromH5Mover.cc
, RemodelConstraintGenerator.cc
, RemoveConstraints.cc
, NtoCConstraintGenerator.cc
, utility.cc
, LayerDesignOperation.cc
, InterlockAroma.cc
, FlxbbDesign.cc
, FilterStructs.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
, SheetConstraintGenerator.cc
, SSPairPotential.cc
, NatbiasStrandPairPotential.cc
, NatbiasSecondaryStructureEnergy.cc
, NatbiasHelixPairPotential.cc
, NatbiasHelicesSheetPotential.cc
, HSPairPotential.cc
, MatchResiduesMover.cc
, MatchResidues.cc
, StepWiseProteinCCD_MultiPoseCloser.cc
, HSSTripletFilter.cc
, HelixPairingFilter.cc
, HelixKinkFilter.cc
, Filter.cc
, BasicFilters.cc
, WaterFeatures.cc
, StructureFeatures.cc
, ProtocolFeatures.cc
, ModelFeatures.cc
, InterfaceFeatures.cc
, HelixBundleFeatures.cc
, util.cc
, RNA_DeNovoParameters.cc
, RNA_FragmentMonteCarlo.cc
, RNA_MinimizerOptions.cc
, RNA_FragmentMonteCarloOptions.cc
, RNA_DeNovoProtocolOptions.cc
, RNA_BasicOptions.cc
, RNA_Relaxer.cc
, RNA_Minimizer.cc
, RNA_LoopCloser.cc
, RNA_JumpMover.cc
, RNA_FragmentMover.cc
, RNA_LibraryManager.cc
, RNA_ChunkLibrary.cc
, ChunkSet.cc
, BasePairStepLibrary.cc
, FARNA_Optimizer.cc
, RNA_BasePairHandler.cc
, RemoveLigandFilter.cc
, EnzRepackMinimize.cc
, EnzFilters.cc
, EnzdesJobInputter.cc
, VoxelSpacingRefinementMover.cc
, ScaleMapIntensities.cc
, ReportFSC.cc
, BfactorFittingMover.cc
, util.cc
, SidechainMinMover.cc
, metrics.cc
, PoissonBoltzmannPotential.cc
, MPDockingMover.cc
, MPDockingSetupMover.cc
, Ramachandran.cc
, MPFindInterfaceMover.cc
, QuickRelaxPartnersSeparately.cc
, NomenclatureManager.cc
, selection.cc
, RNA_ChemicalShiftPotential.cc
, RNA_ChemicalMappingEnergy.cc
, APBSWrapper.cc
, RNA_DMS_LowResolutionPotential.cc
, RNA_DMS_Potential.cc
, adduct_util.cc
, util.cc
, pdb_reader.cc
, CHIEnergyFunction.cc
, util.cc
, RNA_EnergyMethodOptions.cc
, database_io.cc
, RNA_FullAtomStackingEnergy.cc
, RNA_FullAtomVDW_BasePhosphate.cc
, pdb_writer.cc
, FabConstraint.cc
, PreProlineFilter.cc
, ExposedHydrophobicsFilter.cc
, FileConstraintGenerator.cc
, CoordinateConstraintGenerator.cc
, ExtendChain.cc
, Connection.cc
, BridgeChainsOld.cc
, BridgeChains.cc
, StructureData.cc
, Segment.cc
, Picker.cc
, NamedMover.cc
, FoldGraph.cc
, ddGMover.cc
, ddG_main.cc
, SimpleCycpepPredictApplication.cc
, PeptideStubMover.cc
, DeclareBond.cc
, CreateTorsionConstraint.cc
, CreateDistanceConstraint.cc
, CreateAngleConstraint.cc
, CoarseRNA_LoopCloser.cc
, CoarseRNA_Fragments.cc
, APCluster.cc
, SimpleGlycosylateMover.cc
, LinkageConformerMover.cc
, GlycanRelaxMover.cc
, pool_util.cc
, HPool.cc
, BranchAngleOptimizer.cc
, util.cc
, ZincHeterodimerMover.cc
, BackrubProtocol.cc
, BackrubMover.cc
, Ubiquitin_E2C_Modeler.cc
, LHSnugFitLegacy.cc
, LHRepulsiveRampLegacy.cc
, GraftMover.cc
, CDRH3Modeler.cc
, AntibodyModeler.cc
, AntibodyClass.cc
, util.cc
, RestrictToCDRsAndNeighbors.cc
, DisableCDRsOperation.cc
, DisableAntibodyRegionOperation.cc
, AddCDRProfilesOperation.cc
, AddCDRProfileSetsOperation.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
, util.cc
, NativeAntibodySeq.cc
, MutateFrameworkForCluster.cc
, GeneralAntibodyModeler.cc
, StepWiseMonteCarloJobDistributor.cc
, CDRGraftDesignOptions.cc
, AntibodySeqDesignTFCreator.cc
, AntibodyDesignProtocol.cc
, AntibodyDesignMover.cc
, CDRSetOptionsParser.cc
, AntibodyDatabaseManager.cc
, util.cc
, ParatopeSiteConstraintMover.cc
, ParatopeEpitopeSiteConstraintMover.cc
, CDRDihedralConstraintMover.cc
, CDRClusterSet.cc
, CDRClusterMatcher.cc
, CDRsMinPackMin.cc
, AntibodyModelerProtocol.cc
, AntibodyInfo.cc
, AntibodyFeatures.cc
, AntibodyCDRGrafter.cc
, Ab_TemplateInfo.cc
, AnchorMoversData.cc
, Anchor.cc
, PackStatMover.cc
, LoopAnalyzerMover.cc
, InterfaceAnalyzerMover.cc
, ClearCompositionConstraintsMover.cc
, AddCompositionConstraintMover.cc
, ABEGOManager.cc
, SelectResiduesByLayer.cc
, SecondaryStructureSelector.cc
, ResiduePDBInfoHasLabelSelector.cc
, PrimarySequenceNeighborhoodSelector.cc
, PhiSelector.cc
, ParallelBetaPairingPreferenceFilter.cc
, VdWTinkerPotential.cc
, symE.cc
, SplitUnfoldedTwoBodyPotential.cc
, ScoringManager.cc
, ShapeComplementarityCalculator.cc
, MolecularSurfaceCalculator.cc
, sasa.cc
, util.cc
, RNA_SuitePotential.cc
, RNA_TorsionPotential.cc
, NamedAngleConstraint.cc
, LeGrandSasa.cc
, SasaCalc.cc
, Conformation.cc
, record_def_io.cc
, NamedDihedralConstraint.cc
, SiteConstraint.cc
, RecordCollection.cc
, SiteConstraintResidues.cc
, CentroidDisulfidePotential.cc
, AtomProperties.cc
, LipidAccInfo.cc
, chirality_resolution.cc
, DisulfideMatchingDatabase.cc
, LayerSelector.cc
, DisulfideMatchingPotential.cc
, ScoreFileData.cc
, FullatomDisulfidePotential.cc
, FA_ElecEnergy.cc
, MembraneInfo.cc
, RDAT.cc
, FA_GrpElecEnergy.cc
, NMerSVMEnergy.cc
, NMerRefEnergy.cc
, NMerPSSMEnergy.cc
, MultipoleElecEnergy.cc
, MissingEnergy.cc
, MembraneEnvSmoothEnergy.cc
, LK_PolarNonPolarEnergy.cc
, IntermolEnergy.cc
, FreeDOF_Options.cc
, FreeDOF_Energy.cc
, Fa_MbenvEnergy.cc
, DFIRE_Energy.cc
, SugarBackboneEnergy.cc
, MembranePotential.cc
, Membrane_FAPotential.cc
, BackrubSidechainMover.cc
, MPNonHelixPenalty.cc
, MPLipoEnergy.cc
, MPEnvEnergy.cc
, MPCBetaEnergy.cc
, MembraneData.cc
, FaMPEnvSmoothEnergy.cc
, FaMPEnvEnergy.cc
, MembEtable.cc
, util.cc
, MgEnergy.cc
, LoopGraph.cc
, HBondEnergy.cc
, non_scorefxn_exact_model.cc
, GeometricSolEnergyEvaluator.cc
, ExactOccludedHbondSolEnergy.cc
, BluePrint.cc
, SquareWell2Func.cc
, SplineFunc.cc
, CircularSplineFunc.cc
, xray_scattering.cc
, hankel_kiss_fft.cc
, FACTSResidue.cc
, FACTSPotential.cc
, FACTSPose.cc
, GroupElec.cc
, SilentFileLoader.cc
, xray_scattering.cc
, Etable.cc
, CarbohydrateInfo.cc
, Span.cc
, StructFileRepOptions.cc
, FoldTree.cc
, SpanningTopology.cc
, LineMinimizer.cc
, FixbbSimAnnealer.cc
, database_io.cc
, util.cc
, DunbrackRotamer.cc
, ContextIndependentGeometricSolEnergy.cc
, CDRSeqDesignOptions.cc
, AnnealableGraphBase.cc
, SymmetryInfo.cc
, HPatchEnergy.cc
, ResidueArrayAnnealingEvaluator.cc
, ResidueProperties.cc
, SymmetryTransform.cc
, SurfaceEnergy.cc
, make_symmetric_task.cc
, util.cc
, FullModelParameterType.cc
, FullModelParameters.cc
, util.cc
, CopyDofsInfo.cc
, CopyDofs.cc
, MPTerminiPenalty.cc
, util.cc
, pack_missing_sidechains.cc
, RNA_ResidueLevelTask.cc
, ResidueTypeFinder.cc
, ABEGOHashedFragmentStore.cc
, util.cc
, score_function_corrections.cc
, ResidueTypeSetCache.cc
, alt_codes_io.cc
, pose_io.cc
- TR_BGEDGE()
: SurfaceInteractionGraph.hh
- TR_BGNODE()
: SurfaceInteractionGraph.hh
- tr_control()
: PseudocontactShiftEnergyController.cc
, PseudocontactShiftEnergyController_Ts4.cc
, PseudocontactShiftEnergyController_Ts1.cc
, PseudocontactShiftEnergyController_Ts3.cc
, PseudocontactShiftEnergyController_Ts2.cc
- TR_debug()
: PlaceStubMover.cc
- TR_DS()
: RotamerDots.cc
- TR_EDGE()
: SurfaceInteractionGraph.hh
- TR_energies()
: GenericMonteCarloMover.cc
- tr_labels()
: ResonanceList.cc
, CrossPeakInfo.cc
- TR_NODE()
: SurfaceInteractionGraph.hh
- TR_PcsEnergyController()
: PcsEnergyController.cc
- TR_PcsGridSearchParameter()
: PcsGridSearchParameter.cc
- TR_PcsGridSearchParameterManager()
: PcsGridSearchParameterManager.cc
- TR_PYMOL()
: AddZincSiteConstraints.cc
- TR_RD()
: RotamerDots.cc
- TR_RDC()
: RotamerDots.cc
- TR_RDRD()
: RotamerDots.cc
- TR_REMODEL()
: RemodelData.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
- TRDEBUG
: MPI_LoopHashRefine.cc
, MPI_WorkUnitManager_Slave.cc
, MPI_LoopHashRefine_Emperor.cc
, MPI_WorkUnitManager.cc
, MPI_Refinement.cc
, MPI_Refine_Master.cc
, MPI_LoopHashRefine_Master.cc
, MPI_Refine_Emperor.cc
- TRG()
: GraftedStemOptimizer.cc
, GraftOneCDRLoop.cc
- TRhbonds()
: InterfaceAnalyzerMover.cc
- TRinterface()
: InterfaceAnalyzerMover.cc
- TRO()
: GraftMover.cc
- TYPE_NAME()
: JumpSampleData.cc
, AutoCutData.cc
1.8.7
