- a -

• average_rotamers() : Translator.cc

- c -

• chr_chains() : PoissonBoltzmannPotential.cc
• coarse_rotamer() : Translator.cc
• create_rotamer() : Translator.cc

- f -

• find_most_frequent_rotamer() : Translator.cc

- m -

• match_mask() : Translator.cc

- s -

• sqr() : Translator.cc
• sqr3() : Translator.cc
• strip_whitespace() : Translator.cc

- t -

• TR() : adduct_util.cc , CarbohydrateInfo.cc , MPCBetaEnergy.cc , util.cc , symE.cc
• tr() : Energies.cc
• TR() : pdb_dynamic_reader.cc , util.cc , ResidueProperties.cc , RNA_BasePairClassifier.cc , ring_conformer_io.cc , selection.cc
• tr() : SurfaceEnergies.cc , ScoreFunctionFactory.cc , ScoreFunction.cc
• TR() : MembraneInfo.cc , ShapeComplementarityCalculator.cc , MembraneData.cc , CopyDofs.cc
• tr() : RNA_AtomVDW.cc , RNA_LowResolutionPotential.cc , ResidualDipolarCoupling_Rohl.cc , ResidualDipolarCoupling.cc , MinScoreScoreFunction.cc , ResidualDipolarCouplingEnergyRigidSegments.cc , ResidualDipolarCouplingEnergy.cc , DistanceChainbreakEnergy.cc , DipolarCouplingEnergy.cc , ContactOrderEnergy.cc , ChemicalShiftAnisotropyEnergy.cc , LoopCloseEnergy.cc
• TR() : util.cc , Conformation.cc
• tr() : Dssp.cc
• TR() : MPEnvEnergy.cc
• tr() : StrandPairing.cc
• TR() : file_data_fixup.cc
• tr() : UnfoldedStatePotential.cc
• TR() : RingConformerSet.cc
• tr() : StackElecEnergy.cc , DNABFormPotential.cc
• TR() : ScoreFileData.cc
• tr() : 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() : ABEGOManager.cc
• tr() : RNA_Mg_KnowledgeBasedPotential.cc
• TR() : FaMPEnvSmoothEnergy.cc , util.cc
• tr() : RNA_Mg_Energy.cc , DNATorsionPotential.cc
• TR() : Span.cc , LeGrandSasa.cc , RNA_TorsionPotential.cc , RNA_FullAtomVDW_BasePhosphate.cc , RNA_FullAtomStackingEnergy.cc , util.cc , RNA_DMS_Potential.cc , RNA_DMS_LowResolutionPotential.cc , RNA_ChemicalMappingEnergy.cc , RNA_ChemicalShiftPotential.cc , PoissonBoltzmannPotential.cc , SimplePDB.cc , compute_holes_score.cc , NVlookup.cc , MMBondAngleResidueTypeParam.cc , UnfoldedStateEnergy.cc , PoissonBoltzmannEnergy.cc , NMerSVMEnergy.cc , NMerRefEnergy.cc , NMerPSSMEnergy.cc , MissingEnergy.cc , MembraneEnvSmoothEnergy.cc , LK_PolarNonPolarEnergy.cc , IntermolEnergy.cc , FreeDOF_Energy.cc , Fa_MbenvEnergy.cc , DFIRE_Energy.cc , MembranePotential.cc , Membrane_FAPotential.cc , MPTerminiPenalty.cc , MPNonHelixPenalty.cc , MPLipoEnergy.cc , FaMPEnvEnergy.cc , util.cc , SpanningTopology.cc
• tr() : OccludedHbondSolEnergy_onebody.cc
• TR() : MolecularSurfaceCalculator.cc , database_io.cc , LoopGraph.cc , non_scorefxn_exact_model.cc , GeometricSolEnergyEvaluator.cc , ExactOccludedHbondSolEnergy.cc , ContextIndependentGeometricSolEnergy.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
• tr() : ContextDependentGeometricSolEnergy.cc
• TR() : LipidAccInfo.cc , pose_io.cc
• tr() : RNA_VDW_Energy.cc
• TR() : util.cc , APBSWrapper.cc , FullModelParameterType.cc , SasaCalc.cc , util.cc , MembEtable.cc
• tr() : DockingScoreFunction.cc
• TR() : RNA_ResidueLevelTask.cc , pack_missing_sidechains.cc , make_symmetric_task.cc , SurfaceEnergy.cc , HPatchEnergy.cc , RotamerLibrary.cc , DunbrackRotamer.cc , FixbbSimAnnealer.cc , LineMinimizer.cc , FoldTree.cc , SilentFileLoader.cc , RDAT.cc
• tr() : OccludedHbondSolEnergy.cc
• TR() : sasa.cc , FullModelParameters.cc
• tr() : DNAChiEnergy.cc
• TR() : Graph.cc , util.cc , SymmetryInfo.cc
• tr() : PairingsList.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

- u -

• update_mask() : Translator.cc