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• A3BHbsCreatorMoverCOP : a3b_hbs_creator.cc
• A3BHbsCreatorMoverOP : a3b_hbs_creator.cc
• A3BHbsDockDesignMinimizeMoverCOP : a3b_hbs_dock_design.cc
• A3BHbsDockDesignMinimizeMoverOP : a3b_hbs_dock_design.cc
• A3BPeptideBuilderCOP : build_a3b.cc
• A3BPeptideBuilderOP : build_a3b.cc
• abbindingOP : ab_binding.cc
• AbInitio_MPIOP : AbInitio_MPI.cc
• AdjacencyIter : undirected_graph.cc
• AdjacencyIterPair : undirected_graph.cc
• AID : flail.cc
• AIDs : motif_denovo_hb.cc , motif_hash_util.cc
• align_t : format.h
• AnchorFinderMoverOP : AnchorFinder.cc
• AnnotatedFragDataCOP : reportFragments.cc
• AnnotatedFragDataOP : reportFragments.cc
• APDBCMoverOP : AnchoredPDBCreator.cc
• ArchCOP : tcdock.cc
• ArchOP : tcdock.cc
• axis : ZincMinimize.cc , ZincSiteEvaluator.cc , ZincMatchFilter.cc , zinc1_homodimer_design.cc , zinc1_homodimer_setup.cc , zinc2_homodimer_design.cc , zinc2_homodimer_setup.cc