- d -

• ddG_cycles() : design_utils.cc

- f -

• for() : useful_code.cc

- h -

• half_adjust() : FragsToAtomDist.cc
• hbonded() : design_utils.cc , design_utils.hh
• hbonded_atom() : design_utils.cc , design_utils.hh

- l -

• ligand_dock_main() : ligand_dock_impl.cc , ligand_dock_impl.hh

- m -

• main() : main.cc
• mainchains() : useful_code.cc
• MinimizeInterface() : design_utils.cc , design_utils.hh
• mybegin() : SandwichFeatures.cc
• myend() : SandwichFeatures.cc

- n -

• NOESY_CST_FILE_NAME() : IterativeBase.cc
• num_stored_poses() : VIP_Mover.cc

- o -

• OPT_1GRP_KEY() : CanonicalSamplingMover.cc

- p -

• point_mutation() : design_utils.cc

- r -

• rot() : DockingInitialPerturbation.cc , SymDockingInitialPerturbation.cc

- s -

• seq_sep_stage() : ConstraintFragmentSampler.cc
• simple_histogram() : FragsToAtomDist.cc
• SPECIAL_INITIAL_DECOY_PENALTY() : EvaluatedArchive.cc , NormalizedEvaluatedArchive.cc
• SymMinimizeInterface() : design_utils.cc , design_utils.hh

- t -

• trans() : DockingInitialPerturbation.cc , SymDockingInitialPerturbation.cc
• TYPE_NAME() : JumpSampleData.cc , AutoCutData.cc

- w -

• warn_obsolete_flags() : IterativeBase.cc
• which_ostream() : InterfaceAnalyzerMover.cc