Referenced by DougsDockDesignMinimizeMagicMover::apply(), PeptiodMovieMover::apply(), HemeBindingMover::apply(), FloppyTailMover::apply(), HECTMover::apply(), UBQ_E2Mover::apply(), PepMinMover::apply(), A3BHbsDockDesignMinimizeMover::apply(), A3BPeptideBuilder::apply(), CovalentPeptidomimeticDockDesign::apply(), CovalentPeptidomimeticCreator::apply(), MikeLinkerMover::apply(), TrizaolamerDockDesignMinimizeMover::apply(), HbsDesignMover::apply(), OopDesignMover::apply(), PeptoidDesignMover::apply(), UBQ_GTPase_disulfide_Mover::apply(), MPFindInterfaceTestMover::apply(), NativeEnsemble::apply(), MyProtocol::apply(), FloatScMonteCarlo::apply(), TestQuickRelaxMover::apply(), MPDomainAssembly::apply(), aramid_main(), backrub_protocol(), bb_sample(), BBG8T3A_sample(), capri15_relax(), HubDenovo::cen_fold(), cen_fold(), zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), dna_stats(), do_backrub(), do_KIC(), A3BHbsCreatorMover::do_mc(), doit(), erraser_monte_carlo(), gen_pep_bb_frag(), gen_pep_bb_frag_old(), gen_pep_bb_rama(), gen_pep_bb_sequential(), main(), mutate_random_residue(), my_main(), perturb_pep_bb(), refine_fa_pep_bb(), relax_cenrot_pose(), repack_cluster(), run_mc(), run_pep_prep(), RunPepSpec(), ChallengeMover::sample(), sample_rna_dofs_new(), SamplingManager::SamplingManager(), scmove_residue(), small_min_test(), myspace::test_bbgauss(), use_backrub(), and zf_relax_test().
