- f -

• FBBCRSA_RG : FixbbCoupledRotamerSimAnnealer.cc , FixbbLinkingRotamerSimAnnealer.cc

- m -

• mca_RG : MultiCoolAnnealer.cc
• my_RG : ParticleSwarmMinimizer.cc

- r -

• RG : RingConformerSet.cc , MembranePotential.cc , RotamerAssigningAnnealer.cc , PositionDdGInfo.cc , FoldTreeSketch.cc

- s -

• sab_RG : SimAnnealerBase.cc

- t -

• torsion_info : RNA_Util.cc
• tr : DofPassport.cc
• TR : pdb_dynamic_reader.cc , CopyDofs.cc
• tr : SecondaryStructure.cc
• TR : FullModelParameters.cc
• tr : Energies.cc
• TR : SilentFileLoader.cc , UnfoldedStateEnergy.cc
• tr : ContactOrderEnergy.cc , OccludedHbondSolEnergy.cc , BinarySilentStruct.cc
• TR : symE.cc , ShapeComplementarityCalculator.cc , MolecularSurfaceCalculator.cc , SymmetryInfo.cc
• tr : ResidueCoordinateChangeList.cc
• TR : NMerRefEnergy.cc , MMBondAngleResidueTypeParam.cc , RNA_TorsionPotential.cc , RNA_ChemicalShiftPotential.cc , PoissonBoltzmannPotential.cc , SimplePDB.cc , compute_holes_score.cc , FoldTree.cc , sasa.cc
• tr : CoordinateConstraint.cc , LocalPosition.cc
• TR : file_data_fixup.cc
• tr : OccludedHbondSolEnergy_onebody.cc
• TR : NMerPSSMEnergy.cc
• tr : LoopCloseEnergy.cc , ChemicalShiftAnisotropy.cc
• TR : PoissonBoltzmannEnergy.cc , SasaCalc.cc , FreeMoietyEnergy.cc
• tr : FoldTreeSketch.cc
• TR : MembranePotential.cc , Membrane_FAPotential.cc , MembEtable.cc , LoopGraph.cc , non_scorefxn_exact_model.cc , ExactOccludedHbondSolEnergy.cc , SquareWell2Func.cc , SplineFunc.cc , FACTSResidue.cc , FACTSPotential.cc , FACTSPose.cc , MembEtable.cc , Etable.cc , xray_scattering.cc , FA_ElecEnergy.cc , FullatomDisulfidePotential.cc , DisulfideMatchingPotential.cc , DisulfideMatchingDatabase.cc , CentroidDisulfidePotential.cc , SiteConstraintResidues.cc , SiteConstraint.cc , FabConstraint.cc , APBSWrapper.cc , selection.cc , RNA_Util.cc , util.cc , NVlookup.cc , DFIRE_Energy.cc , util.cc , IntermolEnergy.cc , LeGrandSasa.cc
• tr : GeometricSolEnergyEvaluator.cc
• TR : pack_missing_sidechains.cc , make_symmetric_task.cc , SurfaceEnergy.cc , HPatchEnergy.cc , RotamerLibrary.cc , DunbrackRotamer.cc , FixbbSimAnnealer.cc , LineMinimizer.cc , MembraneProteinFactory.cc , SpanFileLoader.cc , SpanFileIO.cc , LipoFileIO.cc , EmbedSearchParamsIO.cc , EmbedDefOptions.cc , EmbedDefIO.cc , util.cc , MembraneResidueFactory.cc , EmbeddingFactory.cc , MembraneProtocolConfigLib.cc , MissingEnergy.cc
• tr : CarbonHBondEnergy.cc , MultiConstraint.cc , SequenceAnnotation.cc , LocalCoordinateConstraint.cc , DockingScoreFunction.cc
• TR : SpanningTopology.cc , MembraneInfo.cc , Conformation.cc , RingConformerSet.cc , ring_conformer_io.cc , database_io.cc , CarbohydrateInfo.cc , adduct_util.cc
• tr : UnfoldedStatePotential.cc , SurfaceEnergies.cc , ScoreFunctionFactory.cc , ScoreFunction.cc , StackElecEnergy.cc , RNA_VDW_Energy.cc , RNA_Mg_KnowledgeBasedPotential.cc , RNA_Mg_Energy.cc , RNA_LowResolutionPotential.cc , RNA_FullAtomStackingEnergy.cc , RNA_AtomVDW.cc , ResidualDipolarCoupling_Rohl.cc , ResidualDipolarCoupling.cc , MinScoreScoreFunction.cc , ResidualDipolarCouplingEnergyRigidSegments.cc , ResidualDipolarCouplingEnergy.cc , DistanceChainbreakEnergy.cc , DipolarCouplingEnergy.cc , NamedAtomID.cc , ChemicalShiftAnisotropyEnergy.cc , EnvCore.cc , StrandPairing.cc
• TR : ABEGOManager.cc , FreeResidueBonusEnergy.cc
• tr : GeometricSolEnergy.cc
• TR : util.cc
• tr : PairingsList.cc
• TR : MembraneEnvSmoothEnergy.cc , RNA_ResidueLevelTask.cc
• tr : ConstraintIO.cc
• TR : FullModelInfoUtil.cc
• tr : DNATorsionPotential.cc , DNAChiEnergy.cc , DNABFormPotential.cc , NamedAtomPairConstraint.cc , DipolarCoupling.cc , Dssp.cc , ContextIndependentGeometricSolEnergy.cc
• TR : util.cc , FullModelParameterType.cc
• tr : BoundConstraint.cc , AtomPairConstraint.cc , AmbiguousNMRDistanceConstraint.cc
• TR : NMerSVMEnergy.cc
• TR_BGEDGE : SurfaceInteractionGraph.hh
• TR_BGNODE : SurfaceInteractionGraph.hh
• TR_DS : RotamerDots.cc
• TR_EDGE : SurfaceInteractionGraph.hh
• TR_NODE : SurfaceInteractionGraph.hh
• TR_RD : RotamerDots.cc
• TR_RDC : RotamerDots.cc
• TR_RDRD : RotamerDots.cc
• TR_SIG : SurfaceInteractionGraph.hh
• TR_STATS : SurfaceInteractionGraph.hh