- a -

• atm_name_pair : CartesianBondedEnergy.hh
• atm_name_quad : CartesianBondedEnergy.hh
• atm_name_single : CartesianBondedEnergy.hh
• atm_name_triple : CartesianBondedEnergy.hh

- b -

• bools : AlignmentAAFinderFilter.hh , AlignmentGapInserterFilter.hh

- c -

• CifFileOP : import_pose.cc , import_pose.hh , cif_reader.hh , cif_writer.cc , cif_reader.cc
• CifParserOP : import_pose.hh , import_pose.cc

- d -

• ddG_data_tuple : DdGScan.hh
• ddgs : ddG_main.cc

- h -

• HelixCapFeaturesCOP : HelixCapFeatures.fwd.hh
• HelixCapFeaturesOP : HelixCapFeatures.fwd.hh

- l -

• LegacyAddStartnodeFragmentsCOP : LegacyAddStartnodeFragments.fwd.hh
• LegacyAddStartnodeFragmentsOP : LegacyAddStartnodeFragments.fwd.hh
• LegacyAppendAssemblyMoverCOP : LegacyAppendAssemblyMover.fwd.hh
• LegacyAppendAssemblyMoverOP : LegacyAppendAssemblyMover.fwd.hh
• LegacyGivenPathAssemblyMoverCOP : LegacyGivenPathAssemblyMover.fwd.hh
• LegacyGivenPathAssemblyMoverOP : LegacyGivenPathAssemblyMover.fwd.hh
• LegacyGreedyAssemblyMoverCOP : LegacyGreedyAssemblyMover.fwd.hh
• LegacyGreedyAssemblyMoverOP : LegacyGreedyAssemblyMover.fwd.hh
• LegacyRepeatAssemblyMoverCOP : LegacyRepeatAssemblyMover.fwd.hh
• LegacyRepeatAssemblyMoverOP : LegacyRepeatAssemblyMover.fwd.hh

- m -

• Matrix : HackAroEnergy.cc , RNA_HelixAssembler.cc , util.cc , util.hh , StepWiseRNA_OutputData.hh , StepWiseRNA_Classes.hh , RNA_DMS_LowResolutionPotential.cc , FloatingBaseClasses.hh , RNA_VDW_BinChecker.hh , StepWiseRNA_PoseSetupFromCommandLine.cc , RNA_LoopCloser.cc , MultipleDomainMover.cc , util.cc , MgWaterHydrogenPacker.cc , MgMonteCarlo.cc , MgHydrater.cc , VdWTinkerPotential.cc , SASAPotential.cc , util.hh , MultipoleElecPotential.cc
• mutations : ddG_main.cc

- o -

• ostringstream_t : init.cc

- p -

• Parent : SingleFragmentMover.cc
• piecewise_poly : ImplicitLipidInfo.cc , AqueousPoreFinder.cc
• point : MetalSiteResidue.cc , ZincSiteFinder.cc , MetalSiteResidue.hh , MatchGrafter.cc , AddZincSiteConstraints.cc
• Pose : MatchGrafter.cc

- s -

• SmotifFeaturesCOP : SmotifFeatures.fwd.hh
• SmotifFeaturesOP : SmotifFeatures.fwd.hh
• String : StrandPairing.cc , HelixPairing.cc , util.cc

- t -

• TorsionList : PhosphateMover.cc

- v -

• ValueList : StepWiseSamplerOneValue.hh
• VecSize : StrandPairing.cc , util.cc
• Vector : MultipoleElecPotential.cc , SASAPotential.cc , VdWTinkerPotential.cc

- x -

• Xform : MotifDockEnergy.cc , MotifDockEnergy.hh
• xyzVec : util.cc