Referenced by myspace::Scheduler.accept_and_report(), actual_disulfide(), add_agc(), add_apc(), add_chi_tags(), protocols::abinitio::JumpSpecificAbrelax.add_constraints(), add_constraints(), add_coordinate_constraints(), MinTestMover.add_coordinate_constraints_to_pose(), add_crystinfo_to_pose(), add_Cu_chains(), add_dhc(), add_dna_states(), apps::public1::scenarios::chemically_conjugated_docking.add_extra_bodies(), add_fnr_constraints(), apps::pilot::SampleSecondaryStructureAlignmentMover.add_gap_constraints_to_pose(), A3BHbsCreatorMover.add_hbond_and_omega_constraints_starting_at_seqpos(), HemeBindingMover.add_initial_constraints(), add_lig_cst(), add_pep_buffer_res(), add_pep_res(), add_scores(), add_side_chains_partialthread(), add_symm_sf4(), add_symm_zns(), add_termini(), MPInterfaceStatistics.add_to_scorefile(), add_triazole_constraints(), add_virtual_res(), add_vrts(), ZincMinimize.add_zinc_constraints(), addcc(), addcyclicconstraints(), adesign(), adjust_pose_chi(), ala_ct(), HDdesignMover.ala_interface(), alapose(), align_backbone_by_chunk(), align_carboxyl_diiron(), align_carboxyl_diiron_OLD(), align_carboxyl_m8(), apps::pilot::AlignChunkMover.align_chunk(), ClusterCycDisulf.align_clusters(), align_native_state(), align_pdbs(), align_pdbs_function(), alignaxis(), alignhelix(), alignment_atoms_in_res(), alignment_torsions_in_res(), all_pair_energies(), all_pose_residues(), alncys(), UBQ_E2Mover.analyze_and_filter(), UBQ_GTPase_disulfide_Mover.analyze_and_filter(), analyze_base_pair_test(), analyze_interface_test(), analyze_poses_for_convergence(), anglestats_local(), dsRNA_grow.append_Aform_residue(), append_jumpless_pose(), append_sequence_to_pose(), CountContact.apply(), AssignClusterToolMover.apply(), EnvToolMover.apply(), MinToolMover.apply(), ScoreMover.apply(), ConstraintToolMover.apply(), RmsfMover.apply(), FitMover.apply(), RDCToolMover.apply(), Protocol_MolecularDynamics.apply(), CalcIrms.apply(), RMSByResStatistics.apply(), BuriedUnsatPolarsFinder.apply(), HbondZinc.apply(), HbondZincBackbone.apply(), xtal_water_bunsat.apply(), zinc_helix_cap.apply(), ZincMinimize.apply(), CollectCoordinates.apply(), GunnTest.apply(), PrintFeatures.apply(), protocols::abinitio::Stage1Sampler.apply(), RotateSAXS.apply(), DougsDockDesignMinimizeMagicMover.apply(), PeptoidDihedralGrabber.apply(), PeptiodMovieMover.apply(), PeptoidRotamerRecoverer.apply(), CartRefineWrapperMover.apply(), CenRelaxMover.apply(), dsRNA_grow.apply(), MirrorSymmTest.apply(), AbInitio_MPI.apply(), HemeBindingMover.apply(), HemeReplace.apply(), GraftDesignCDRs.apply(), protocols::antibody::design::AntibodyDesignMoverGenerator.apply(), RelaxCDRsMover.apply(), TestMMOP.apply(), InterfaceFeaturesTests.apply(), myspace::GraftTester.apply(), SuperDeviationMover.apply(), ComputeProfileMover.apply(), PrintSequenceMover.apply(), ConstraintMinimizer.apply(), InteractionDistMinimizer.apply(), ConstraintStatsMover.apply(), SpartaSuperDeviationMover.apply(), InjectorMover.apply(), khSandbox.apply(), KHSandbox.apply(), abbinding.apply(), mtransferase.apply(), PhDocking.apply(), PhProtocol.apply(), DesignGlycansProtocol.apply(), GlycomutagenesisProtocol.apply(), LoopHash_Analyze.apply(), RDCScoreMover.apply(), LocalRmsd.apply(), PairDistance.apply(), PickBAB.apply(), Sasa.apply(), DeleteSegments.apply(), SetupHotspotMover.apply(), ElecDensMinPackMinMover.apply(), FloppyTailMover.apply(), ForgetMover.apply(), HECTMover.apply(), sasa_qdMover.apply(), UBQ_E2Mover.apply(), PepMinMover.apply(), IAMover.apply(), SymFixbbMover.apply(), XMLprinterMover.apply(), FoldTreeOutputter.apply(), HelicalPdbGeneratorMover.apply(), InterfaceStrandFinderMover.apply(), RDF_Mover.apply(), ChiMover.apply(), CycBBMover.apply(), MoveThenFixH.apply(), MoveThenFixHMin.apply(), LigChiMover.apply(), DuboisChiMover.apply(), BBMover.apply(), HolesTrainingDataMover.apply(), SymRBMover.apply(), SimpleBBMover.apply(), apps::pilot::AlignChunkMover.apply(), apps::pilot::MultiTemplateAlignChunkMover.apply(), apps::pilot::CustomStarTreeMover.apply(), apps::pilot::CustomFragmentMover.apply(), apps::pilot::HelixMover.apply(), ChallengeMover.apply(), PBPotentialMover.apply(), apps::pilot::SampleSecondaryStructureAlignmentMover.apply(), SilentProlineFixMover.apply(), InterfaceDDGMover.apply(), A3BHbsCreatorMover.apply(), A3BHbsDockDesignMinimizeMover.apply(), A3BPeptideBuilder.apply(), CovalentPeptidomimeticDockDesign.apply(), CovalentPeptidomimeticCreator.apply(), B3AADihedralGrabber.apply(), MikeLinkerMover.apply(), TorsionVectorMover.apply(), TriazoleCreator.apply(), TrizaolamerDockDesignMinimizeMover.apply(), Packing_energies.apply(), SSM_energies.apply(), MyMover.apply(), JDmover.apply(), MyScoreMover.apply(), ComputeSAXSSpectrum.apply(), RescorePDDF.apply(), PrintPDDF.apply(), RescoreSAXS.apply(), FaSolReporter.apply(), MinTestMover.apply(), PerturbStruct.apply(), CrystHbondsReporter.apply(), LigandDockingHbondsReporter.apply(), SetupMover.apply(), JDtestmover.apply(), LDConverterMover.apply(), HotspotPlacementMover.apply(), LoopHashRelax_Sampler.apply(), protocols::moves::FragCaptureMover.apply(), Foldptn.apply(), MakeCanonicalHelix.apply(), SampleTiltProtocol.apply(), ColorByLipidType.apply(), FindOptimalHydrophobicThk.apply(), LigandRepackMinimizeProtocol.apply(), hackLAMMover.apply(), CalcsTestMover.apply(), MinPackMinMover.apply(), MinCenrotMover.apply(), CenRotRelaxMover.apply(), RosettaHolesMover.apply(), IdentifyCDRClusters.apply(), DockGlycansProtocol.apply(), GlycanClashCheckMover.apply(), APDBCMover.apply(), AnchorFinderMover.apply(), ExtractATD.apply(), HbsDesignMover.apply(), OopDesignMover.apply(), PeptoidDesignMover.apply(), MakeSegmentFileMPI.apply(), RNA_ScoreMover.apply(), ExposedStrandMover.apply(), HDdesignMover.apply(), HDmakerMover.apply(), CaToAllAtom.apply(), UBQ_GTPase_disulfide_Mover.apply(), BacksideHbondFinderMover.apply(), MetalSiteFinderMover.apply(), SeqBBTorSRFD.apply(), HemaggTrimer.apply(), MotifDock.apply(), CalcCdrRms.apply(), PackingAngle.apply(), CloseContactWithResidue.apply(), Designer.apply(), TNM.apply(), ZincSiteEvaluator.apply(), CustomMover.apply(), DetectSymmetry.apply(), FragmentBasedDesign.apply(), SwapElementsMover1.apply(), SwapElementsMover2.apply(), MPFindInterfaceTestMover.apply(), MPframeworkTestMover.apply(), MPframeworkTest1Mover.apply(), ClosureMover.apply(), BreadthMover.apply(), MyApp.apply(), NativeEnsemble.apply(), Benchmark.apply(), RamaTestMover.apply(), ScTrials.apply(), HBondReporter.apply(), MotifScanMover.apply(), MembraneViewMover.apply(), MembraneMinMover.apply(), MembraneSfxnMover.apply(), MembraneDockingxMover.apply(), MembraneRelaxMover.apply(), MembraneSampleMover.apply(), MembraneTransformMover.apply(), BBG_Cyclic_Mover.apply(), MyProtocol.apply(), BUNS_Output.apply(), zinc1_homodimer_design.apply(), CrystDesign.apply(), CrystRelax.apply(), CrystCluster.apply(), CrystFFTDock.apply(), MPInterfaceStatistics.apply(), TestQuickRelaxMover.apply(), MPFoldingMover.apply(), LoadMembraneMover.apply(), ViewMembraneProteinMover.apply(), ClearPoseHeader.apply(), CenRotSidechainMover.apply(), CenRotCanonicalMover.apply(), CenRotRBRelaxMover.apply(), CenRotDockingMover.apply(), zinc2_homodimer_design.apply(), zinc2_homodimer_setup.apply(), MPDomainAssembly.apply(), Minimize.apply(), ExemplarMover.apply(), NCMinimize.apply(), myspace::Evaluator.apply(), StepwiseTorsionMover.apply(), ConcertedTorsionMover.apply(), protocols::moves::SimpleCstMover.apply(), BondedRNA_Mover.apply(), ZF_PatchupMover.apply(), MPScoreFunctionFingerprintMover.apply(), complex_interface_optimize.apply(), generate_hbond_geometry.apply(), ScoreFunctionFingerprintMover.apply(), compute_Irmsd.apply(), run_score_patchdock_hotspot.apply(), run_score_hotspot.apply(), protocols::abinitio::PcaEvaluator.apply(), protocols::abinitio::ShowViolation.apply(), protocols::abinitio::ComputeTotalDistCst.apply(), apply_all(), apply_all_frags(), apply_angle_set(), apply_backbone(), apply_backbone_rotamer(), apply_filter_base_stack_direction(), apply_ideal_A_form_torsions(), protocols::jd2::RECONMPIJobDistributor.apply_linking_constraints(), apply_mask(), apply_nucleoside(), apply_nucleoside_torsion(), protocols::jd2::RECONMPIJobDistributor.apply_parsed_protocol(), apply_rigid_body_settings(), apply_south_syn_to_dinucleotide_pose(), apply_suite_torsion(), apply_suite_torsions(), apply_torsion_set(), aramid_main(), aro_pack_pdbstats_from_pose(), IAMover.assign_IA_mover(), assign_rigid_body_settings_to_clusters_test(), assign_stack_faces(), atom_tree_torsion_test(), atom_vdw_test(), atoms_have_bond_to_bonded_atoms(), atoms_have_mutual_bond_to_atom(), average_degree(), avg_ca_position(), MinPackMin.backbone_minimization(), backrub_min_test(), backrub_protocol(), ClosureMover.balanced_apply(), base_doublet_rmsd_test(), base_pair_to_base_pair_test(), bb_bins_from_pose(), bb_sample(), InterfaceStrandFinderMover.bb_score(), ExposedStrandMover.bb_score(), HDmakerMover.bb_score(), BBG8T3A_sample(), benchmark_contacts(), benzene_pair_score_test(), betapeptide_setomega(), betapeptide_setphi(), betapeptide_setpsi(), betapeptide_settheta(), HBondReporter.bfactor(), bk_test(), block_stack_test(), bp_score_calibrate(), brt_clash(), brute_force_matcher(), build_and_score_res1_against_res2(), build_asn_motifs(), build_bb_independent_rotamers(), build_helix_test(), build_next_nucleotide_test(), build_on_helix(), build_polymer(), HbondZinc.build_rotamers(), build_toy_pose(), bump_check(), buns_for_pose(), buns_stats(), BuriedUnsatPolarsFinder.bunsat_acc_nbr_residue_check(), BuriedUnsatPolarsFinder.bunsat_donor_nbr_residue_check(), bunsats(), BuriedUnsatPolarsFinder.bunsats_thorough_check(), byres_analysis(), bzip_test(), MatchSet.c2_clash_check(), MatchSet.c2_iface_check(), CA_cst_generator(), CA_distance(), cal_distance(), calc_B_values(), HDdesignMover.calc_bb_E(), calc_burial(), calc_contacts(), calc_dihedral_rms(), PhDocking.calc_energies(), abbinding.calc_energies_and_sasa(), calc_rama(), calc_rama2b(), calc_rama_scores(), calc_RF(), calc_rms_test(), calc_rmsd_test(), calc_rmsf_and_avrg(), PairDistance.calc_rsd_sasa(), calc_sasa(), calc_shape_complementarity(), ConstraintStatsMover.calc_stats(), CalcsTestMover.calc_stuff(), GlycanClashCheckMover.calculate_atom_clashes(), calculate_average_residue_scores(), calculate_binding_energy(), calculate_distances(), DistanceMatrix.calculate_distances(), calculate_hASA_by_type_and_attractiveE(), calculate_hASA_by_type_and_exposure(), calculate_hASA_by_type_and_nbcount(), calculate_helical_parameters(), calculate_helical_parameters_helper(), calculate_helical_tail_variance(), calculate_hydrophobic_accessible_surface_area(), MPInterfaceStatistics.calculate_interfaces(), calculate_max_rmsd_variance(), calculate_min_tm_variance(), calculate_pairwise_RMSD(), calculate_percent_hydrophobic_distribution(), calculate_percent_hydrophobic_stats(), calculate_rmsd_variance(), calculate_sasa(), calculate_sheet_pct(), calculate_surface_exposure(), calculate_theoretical_RNA_length(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), calculate_tm_variance(), TorsionList.calculate_torsions(), calculate_total_hASA_within_distance_avg_values(), calculate_total_hASA_within_distance_avgresiduevalues_allnbs_conditionalonnumnbs(), calculate_total_hASA_within_distance_exact_hASA_values(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs_exposedornot_conditionalonnumnbs(), calculate_total_hASA_within_distance_miniSASAvalues_allnbs_exposedornot_conditionalonnumnbs(), calculateInterfaceScore(), capri15_relax(), capri_t033_centroid_trim_dock_test(), capri_t033_loop_test(), capri_t033_trim_dock_test(), HbondZincBackbone.carbonyl_hbond_search(), myspace.CArmsd_and_superimpose_pose(), CAtrace.CAtrace(), CB_distance(), ccd_close_loop(), ccd_close_zf_chainbreak(), ccd_loop_close(), ccd_test(), cen_fold(), cendnapose_from_file(), cenpose_from_file(), apps::pilot::SampleSecondaryStructureAlignmentMover.center_of_mass(), center_of_mass(), center_pose_at_origin(), centroid_rescore_test(), centroid_scores_destroys_pose(), ch_o_pdbstats_from_pose(), chain_begin(), chain_coords(), chain_end(), TwoChainInterface.chain_letter_to_number(), TwoChainTenANeighbors.chain_letter_to_number(), change_floating_sc_geometry(), change_floating_sc_geometry_reverse(), check_chi_correct(), myspace.check_clash(), check_clash(), check_filter_base_stack(), protocols::abinitio::JumpSpecificAbrelax.check_filters(), check_for_contacts(), check_for_contacts_and_output_jump_o2prime(), check_for_contacts_and_output_jump_phosphate(), BacksideHbondFinderMover.check_for_hbonds(), check_jump(), check_lengths(), check_protein_rna_clash(), check_sequence(), check_structures(), checked_steal_fragment(), chi_stats_test(), ChiMover.ChiMover(), chis_from_pose(), cl_score(), ClashCheck.clash_check(), MatchSet.clash_check(), clash_check_bb(), ClashCheck.clash_check_naive(), MatchSet.clash_check_naive(), ClashCheck.clash_check_trimer(), SwapElementsMover1.clash_monomer(), cleanup_dna_chains(), HDdesignMover.cloak_and_setup(), close_chain_breaks(), protocols::abinitio::JumpSpecificAbrelax.close_loops(), close_loops(), ClosureMover.ClosureMover(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), cluster_rotamers(), cluster_silent_file_data(), coarse_close_loop_test(), coarse_frag_test(), coarse_rb_test(), coarse_rna_denovo_test(), coarse_to_full_test(), myspace.collect_silent(), collect_stats(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), color_by_lj_test(), MatchSet.com(), compare_dna_energies(), compare_energies(), StepWiseJobQueen.complete_larval_job_maturation(), FixbbJobQueen.complete_larval_job_maturation(), RelaxJobQueen.complete_larval_job_maturation(), compute(), compute_chem_shift_RMSD(), compute_chi(), MainWindow.compute_com_vect(), compute_folding_energies(), compute_motif_score(), compute_sasa(), compute_windowed_rama(), GunnTest.computeGunnTuples(), concave_shell(), cone_cen_nc_calculator(), cone_FA_nc_anyatom_calculator(), cone_FA_nc_calculator(), cone_FA_nc_calculator_amide(), connectivity_test(), dsRNA_grow.constrain_and_minimize(), HbondZinc.constrain_zinc(), HbondZincBackbone.constrain_zinc(), contact_model_prediction(), myspace::Scheduler.control_schedule(), convert_silent_file_to_pose_data_list(), convert_to_coarse_test(), convert_to_native_test(), copy_DOFS_local(), copy_rotamerized_torsions(), copy_segment_bb(), copyresidueposition(), correct_dunbrack(), count_backbone_atoms(), count_bins(), SwapElementsMover2.count_clashes(), count_contacts(), count_int_CBs_clashes(), count_neighbors(), create_and_score_fragments(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_dihedral_constraint(), create_extra_output(), HECTMover.create_extra_output(), apps::public1::scenarios::chemically_conjugated_docking.create_extra_output(), create_fullcoverage_hbgeoms_to_measure(), create_mingraph_for_focused_residue_pair(), create_random_pose(), MPDomainAssembly.create_residue_from_resn(), create_rna_benchmark_test(), create_rna_vall_torsions_test(), create_starting_template(), create_theozyme_pdb(), ui::task.create_viewer_for_file(), cs_rosetta_rna_pdb(), cst_relax_test(), cst_test(), DockFragmentsMover.cut_from_map(), cyclic_all_atom_rms(), cyclic_all_atom_rmsd(), cyclic_ca_rms(), cyclic_ca_rmsd(), cyclic_perm(), cyclize_pose(), dab_sasa(), ddg(), decompose(), HBondReporter.decoyify(), define_interface(), define_movemap_extending_chain(), define_states_test(), A3BHbsCreatorMover.delete_extra_residues(), delete_protein_from_pose(), delete_RNA_from_pose(), delete_test(), delta_chi_correction_test(), density_grid_search(), densityTools(), derive(), derive_MoveMap_from_cluster_lst(), design(), design_1comp(), CrystDesign.design_cycle(), design_dyad(), design_homodimer(), design_pose_motifs_only(), zinc1_homodimer_design.design_symmetric_homodimer_interface(), zinc2_homodimer_design.design_symmetric_homodimer_metal_interface(), design_test(), protocols::jd2::RECONMPIJobDistributor.design_this_nodes_pose(), design_using_resfile(), InterfaceDDGMover.determine_central_seqpos(), determine_delx_dely_delz_alpha_beta_gamma(), DockGlycansProtocol.determine_docking_partners(), determine_if_at_local_minimum_analytic(), determine_if_at_local_minimum_numeric(), InterfaceDDGMover.determine_if_complex(), InterfaceDDGMover.determine_if_wt(), InterfaceDDGMover.determine_mutation(), devel_main(), dinucleotide_test(), apps::pilot.discontinued_lower(), apps::pilot.discontinued_upper(), dist_matrix_test(), DistanceMatrix.DistanceMatrix(), GlycomutagenesisProtocol.disulfide_treatment(), diversify_sam_loop_test(), dna_chain_check(), dna_coupled_rotamer_design_test(), dna_deriv_test(), dna_deriv_test_old(), dna_design_test(), dna_design_test_old(), dna_dr_loop_test(), dna_dr_test(), dna_geometry(), dna_io_test(), dna_motif_matcher(), dna_nbr_radii_test(), dna_specificity_test(), dna_stats(), dna_test(), dnabase_test(), do_backrub(), do_color_by_score(), do_cycpep_analysis(), protocols::abinitio::JumpSpecificAbrelax.do_distributed_rerun(), do_KIC(), A3BHbsCreatorMover.do_mc(), do_minimization(), PerturbStruct.do_mutate(), protocols::abinitio::JumpSpecificAbrelax.do_rerun(), CrystDesign.do_reversion(), ChallengeMover.do_rigid_body_moves(), do_rtmin(), do_sc_min(), do_sc_relax(), do_the_match(), do_work(), dock(), InterfaceStrandFinderMover.dock_strands(), doit(), dostuff(), dot_sasa(), double_helix_test(), double_linked_fold_tree(), double_unlinked_fold_tree(), ChallengeMover.downstream_residues_from_jump(), apps::pilot.downstream_residues_from_jump(), drrafter_error_estimation(), dump_bundle_pose(), dump_clash_pdb(), dump_ddg_pdb(), dump_dna_kinemage(), dump_efactor_pdb(), dump_energy_kinemage(), dump_hbond_pdb(), dump_hbonds(), dump_pair_pose(), dump_pose(), dump_pose_diff(), CrystFFTDock.dump_transformed_pdb(), dumpsym(), dumpsym2(), dumpsym6(), each_aa_test(), easy_loop_model_test(), easy_target_test(), endo_test(), enforce_atoms_coplanar(), enforce_triazole_distance(), ensure_cyclic(), entropy_calculate_test(), env_sugar_test(), erraser_monte_carlo(), hbond_geom_strat.evaluate(), DisulfideBondEnergy.evaluate(), myspace.evaluate_and_write(), ZincSiteEvaluator.evaluate_coordinating_res_energies(), ZincSiteEvaluator.evaluate_coordinating_res_types(), ZincSiteEvaluator.evaluate_ligand_sasa(), ZincSiteEvaluator.evaluate_mutations_native(), evaluate_score(), ZincSiteEvaluator.evaluate_zinc_geometry(), ZincSiteEvaluator.evaluate_zinc_neighbors(), ZincSiteEvaluator.evaluate_zinc_second_shell(), myspace::Evaluator.Evaluator(), apps::pilot::momeara::HBondConformation.example_OH_pose(), exclude_loop_residues(), ui::network::Bowman.execute(), expand_chi_for_silent_structs(), extend_loop(), extending_chain(), extract_pdbs_test(), extract_scores(), extract_ss_chunks_from_seq(), fa_cenpack_pdbstats_from_pose(), fa_refine_and_design(), fa_scorefxn_test(), facts_test(), fast_clash_check(), figure_out_domain_map(), figure_out_domain_neighbors(), figure_out_fold_tree(), figure_out_icoord_test(), figure_out_secstruct(), figure_out_stems(), files_for_openMM_test(), fill_chainTORS_info(), XMLprinterMover.fill_designable_set(), fill_designable_set(), fill_hbond_e(), fill_hbond_neighbors(), fill_num_neighbors(), XMLprinterMover.fill_packable_set(), fill_pose_list(), MPInterfaceStatistics.fill_vectors_with_data(), CrystDesign.filter_and_report(), filter_combine_long_loop(), PhProtocol.finalize_res_list(), CapriTotalEnergy.finalize_total_energy(), find_backbone_rts_in_pose(), myspace.find_best_projection(), find_buried_unsatisfied_polars(), find_close_motifs(), find_close_parents(), find_closest_points(), find_cutpair_alignments_in_pose(), find_disulfides(), find_dna_chainbreaks(), find_dna_rotamers(), find_hppatches_distance(), find_hppatches_nb_graph(), TwoChainInterface.find_interface(), TwoChainTenANeighbors.find_interface(), HemeReplace.find_ligand(), find_neighbors(), HbondZinc.find_neighbors(), HbondZincBackbone.find_neighbors(), find_neighbors_directional(), find_next_repeat_inflection_point(), find_nonlocal_segment_alignments_in_pose(), find_residues_around_mutation(), find_rsd_nbrs(), HbondZinc.find_zinc(), HbondZincBackbone.find_zinc(), ZincSiteEvaluator.find_zinc_site(), finely_sample_base_pair_test(), fix_alpha_for_pack_phosphate(), BBG_Cyclic_Mover.fix_disulf(), fix_sugar_bond_angles_CLOSE_BOND(), fix_sugar_bond_angles_EMPIRICAL(), fixbb_design(), fixH(), fold_tree_generator(), frag_extract_test(), full_protein_repack(), ga_main(), ClosabilityScore.gap_bound_cst_score(), gather_info_all_repeats(), gather_info_canonical_repeats(), gather_repeat(), gather_repeats(), gen_fold_tree_for_nbr_segments(), gen_pep_bb_frag(), gen_pep_bb_frag_old(), gen_pep_bb_rama(), gen_pep_bb_sequential(), genborn_test(), general_initialize(), generate_combined_model(), SetupHotspotMover.generate_csts(), generate_disulfide_conformations(), protocols::antibody::design::AntibodyDesignMoverGenerator.generate_dock_high_res(), protocols::antibody::design::AntibodyDesignMoverGenerator.generate_dock_low_res(), protocols::antibody::design::AntibodyDesignMoverGenerator.generate_minimizer(), protocols::antibody::design::AntibodyDesignMoverGenerator.generate_relax(), protocols::antibody::design::AntibodyDesignMoverGenerator.generate_repack_antigen_ab_interface(), protocols::antibody::design::AntibodyDesignMoverGenerator.generate_repack_cdrs(), HBondReporter.get_aa_counts(), MPInterfaceStatistics.get_aa_statistics(), get_aa_torsion_string(), get_aligned_crd(), get_all(), get_all_1helix_docks(), get_all_2helix_docks(), get_aln_resi(), get_angle_sets(), get_angles(), get_atom_lk_burial(), get_atom_lk_energy(), get_atom_packing_score(), get_atom_vdw(), get_atomatom_rt(), get_attachment_point_string(), get_avail_don_acc(), MPInterfaceStatistics.get_avg_charge(), MPInterfaceStatistics.get_avg_hydrophobicity(), MPInterfaceStatistics.get_avg_number_charges(), get_backbone(), get_base_pair_coordinate_system(), get_base_steps(), get_basepair_atoms(), get_binding_score(), get_bonded_rna_dof_ids(), get_bps_tag(), get_ca_distance(), get_ca_distances(), protocols::antibody::design::AntibodyDesignMoverGenerator.get_cdrs_movemap_with_overhang(), TwoChainInterface.get_chain_terminii_(), TwoChainTenANeighbors.get_chain_terminii_(), MPInterfaceStatistics.get_chains_from_cmd(), get_change_in_distance(), MPInterfaceStatistics.get_charge(), get_chis(), get_chis_complicated(), get_clash_pairs(), get_complex_score(), get_contact_devs(), get_contact_list(), get_contacts(), get_csts_from_pose(), myspace.get_data_index(), get_ddG(), get_distance(), get_distance_around_rna_base(), get_distance_endpoint(), get_distance_midCA(), get_distances(), get_distances_around_rna_backbone(), get_dm(), get_dm_features(), get_elec_score(), get_hb_info(), get_hb_srbb_score(), get_hbond_score(), get_helices(), get_helix_axis(), apps::pilot::HelixMover.get_helix_center(), get_helix_center(), apps::pilot::HelixMover.get_helix_centers(), apps::pilot::HelixMover.get_helix_vectors(), get_helixCAInContact(), get_holes_score(), MPInterfaceStatistics.get_hydrophobicity(), get_icoor(), get_info_test(), MPInterfaceStatistics.get_inout_orientation(), get_interface_energies(), get_interface_residues(), CrystDesign.get_interface_residues(), get_interface_type(), CrystFFTDock.get_interfaces_allatom(), get_jump_to_position(), BBG_Cyclic_Mover.get_L_move(), get_linker_dihedrals(), get_lj_atom_score(), apps::pilot::AlignChunkMover.get_local_sequence_mapping(), zinc_stats::ZincStatisticGenerator.get_local_zn_positions_for_residue(), get_localbfacs(), get_logL_DMS(), get_loop_to_helix_points(), get_min_frag_rmsd(), get_moment_of_inertia(), get_motif_hits_common(), get_movable_jumps(), myspace.get_movemap(), protocols::antibody::design::AntibodyDesignMoverGenerator.get_movemap_from_task(), get_mutations_from_file(), get_n_bb_hbonds(), get_n_hbonds(), get_n_hbonds_from_pair(), get_n_mer_maltose(), get_n_mer_polyalanine(), get_n_pep_nbrs(), get_n_sc_hbonds(), get_nearest_loop_to_helix(), get_neighbor_residues(), CrystDesign.get_neighbor_residues(), get_neighbor_subs(), get_nucleoside(), get_num_nbrs(), MPInterfaceStatistics.get_number_charges(), MPInterfaceStatistics.get_number_hbonds(), MPInterfaceStatistics.get_number_of_residues(), MPInterfaceStatistics.get_number_pi_stacking(), get_numeric_deriv(), get_omg_from_rsd(), get_opte_data(), get_packing_score(), get_perresE(), get_phi_from_rsd(), get_pose_and_numbering(), get_pose_chains(), get_pose_energy_breakdown(), get_psi_from_rsd(), get_radius(), CrystFFTDock.get_radius_of_pose(), TestQuickRelaxMover.get_repack_residues(), get_repl_xyz(), get_res_avg_lk_burial(), get_res_data_ss(), get_res_hbond_bb_score_raw(), get_res_water_energy(), get_residue_key(), MPInterfaceStatistics.get_residue_size(), get_residue_xyz_list(), get_resmap(), myspace.get_resmap(), get_rmsd(), get_rmsd_debug(), get_RNA_binding_residues(), get_rot_score(), get_rot_set(), get_rotamers(), get_rotset(), get_rsdrsd_jump(), ClosabilityScore.get_rt_over_leap(), get_sasa(), get_sc(), get_sc_automorphic_rmsd(), get_sc_rmsd(), get_scanres(), get_score_terms(), get_second_2_helices(), get_sheets(), get_sidechain_rmsd(), get_simple_RNA_protein_fold_tree(), MPInterfaceStatistics.get_size(), get_sphere_xyz(), get_ss(), get_subPose(), get_subpose(), MPInterfaceStatistics.get_surface_complementarity(), get_tenA_neighbor_residues(), get_three_atom_sc_rmsd(), get_tht_from_rsd(), get_torsion_set(), myspace.get_touched_res(), get_unbound_protein_score(), get_useful_fold_trees_for_gcc185(), BBG_Cyclic_Mover.get_VdRdPhi(), get_water_hbond_score(), get_xyz(), get_zn_axes(), glu_ct(), gradient_magnitude_for_conformation(), gradual_minimization(), HbondZinc.graft_match(), HbondZincBackbone.graft_match(), graft_pdb(), graphics_main(), CrystDesign.greedy_revert_unsats(), grid_matcher(), zinc1_homodimer_design.gridsearch_rollmove_angles(), hack_create_rotamer_string(), hard_minimize(), hard_pack(), harvest_motifs(), harvest_motifs_one(), HbondZincBackbone.has_backbone_hbond(), has_cis_bonds(), has_clash(), hb_score(), HbondZinc.hbond_constraint(), apps::pilot::momeara::HBondConformation.hbond_param_sweep(), hbond_stats(), helix_axis(), helix_from_sequence(), helix_minimize(), helix_ST(), hermann_phase_two(), hermann_phase_two_minimize(), hessian_estimate(), homolog_finder(), hxl_test(), icoor_test(), idealize_tf_pose(), identify_targeted_positions(), if(), MatchSet.iface_check(), iface_check_c3(), ifc_clash(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his_clamp(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), import_and_dump_pdb(), MatchBase.init(), CenRotRBRelaxMover.init(), CenRotDockingMover.init(), AbInitio_MPI.init_on_new_input(), HECTAllMover.init_on_new_input(), HECTUBQMover.init_on_new_input(), FloppyTailMover.init_on_new_input(), init_torsions_still_present(), initialize_base_pair(), protocols::abinitio::JumpSpecificAbrelax.initialize_constraint_forest(), initialize_fa_rep(), initialize_from_pdb(), initialize_native_pose(), initialize_o2prime_pack(), initialize_peptide(), initialize_pose(), ChallengeMover.initialize_pose(), initialize_rigid_body_sampler(), initialize_sequence_mask(), insert_chunk(), protocols::abinitio::JumpSpecificAbrelax.insert_template_frags(), interface_between_chains(), interface_energymap(), interface_repack_test(), interface_residue_ddg(), interface_residues(), intra_dna_stats(), is_atom_clash(), is_clash(), GlycanClashCheckMover.is_clashing(), ExposedStrandMover.is_exposed(), is_interface_bbatom(), is_interface_heavyatom(), is_interface_heavyatom_pair(), is_interface_residue(), is_new_cluster_center_rotamer(), is_new_cluster_center_second_stage(), is_new_cluster_center_xyz(), is_regular_helix(), InterfaceStrandFinderMover.is_strand_exposed(), IsctFast.IsctFast(), zinc_stats::ZincStatisticGenerator.iterate_over_residues(), jitter_and_minimize(), journal_club_syn_chi(), juke_sam_pos(), juke_sam_test(), ChallengeMover.jumps_from_pose(), protocols::antibody.keep_cdr(), KIC_loop_close(), apps::pilot::KicSandbox.KicSandbox(), kono_sarai_stats(), kono_sarai_zscore(), lariat_modeling(), ligand_test(), ligrot_test(), linmin(), lk_ball_wtd_deriv_test(), load_bb_torsions_into_vector(), load_coords(), HBondReporter.load_job_data(), load_pose(), loop_closure_test(), loop_modeling_test(), loop_rebuilding_test(), LoopBuild_main(), myspace::Scheduler.loophash_search(), loophash_search(), luxr_setup(), luxr_test(), main(), A3BHbsCreatorMover.make_a3b_pose(), make_bonded_rna_move(), make_coiled_coil(), apps::pilot::momeara::HBondConformation.make_conformation(), TCDock.make_dimer(), make_dna_only_pose(), make_dock_olig(), make_frag_set(), make_fragments(), make_helix(), make_motif_task(), make_move_map(), make_native_olig(), TCDock.make_pentamer(), make_pose(), make_sequence_change(), make_symm_data(), TCDock.make_tetramer(), TCDock.make_trimer(), make_two_trimers(), makerots(), mask_out_loop(), match_main(), MatchLig.MatchLig(), MC_run(), measure_sequence_recovery(), methane_pair_score_test(), mg_hires_pdbstats_from_pose(), mg_modeler_test(), mg_pdbstats_from_pose(), mg_pdbstats_test(), minimize(), dsRNA_grow.minimize(), minimize_all_sidechains(), minimize_and_score(), minimize_helix(), minimize_pdb(), minimize_poses(), minimize_protocol(), minimize_sidechain(), minimize_test(), minimize_to_close(), minimizer_test(), mismatch_test(), mm_pack_test(), protocols::antibody.model_cdrs(), modeler_closure_test(), modeler_map_test(), modify_foldtree(), morph_by_internal_coords(), morph_pdbs_test(), motif_dna_packer_design(), motif_scan(), motif_score_pose(), MPframeworkTest1Mover.move_apart(), move_it(), move_jump(), move_pose(), MPframeworkTest1Mover.move_together(), MoveThenFixHMin.MoveThenFixHMin(), MSA_design(), MSA_design_main(), multiple_variant_type_test(), InterfaceDDGMover.mutate_and_relax(), mutate_random_residue(), zinc_stats::ZincStatisticGenerator.mutate_residue(), BacksideHbondFinderMover.mutate_residue(), mutate_residue(), mutate_residues_wrapper(), mutate_to_ala(), my_main(), mydumppdb(), myMC.myMC(), myoptH(), ClosureMover.naive_apply(), nc_score(), neighbor_count(), MembraneViewMover.new_fastrelax_cycle(), new_sc(), newer_sc(), myspace::Scheduler.NM_linesearch(), non_chain_coords(), normalize_residue_sasa(), not1_loop_test(), not1_test(), nucleobase_probe_score_test(), num_chains(), o2prime_packer(), old_simple_conformation_test(), BreadthMover.omega_apply(), ui::widgets::PoseEditor.on_action_open_pose_triggered(), ui::network::Bowman.on_bowman_thread_progress_data_received(), ui::network::Bowman.on_bowman_thread_result_received(), ui::widgets::PoseEditor.on_functions_double_clicked(), MainWindow.on_nonparametric_geometry_moved(), one_chain_MC_sampling(), one_chain_ST_MC(), oneChainPose(), opt_bicelle_params(), opt_double_vesicle_params(), opt_vesicle_params(), SSM_energies.optimization_loop(), optimize_pose(), optimize_weights(), output_angles(), output_backbone_stats(), output_benchmark_stuff(), output_canonical_base_pair_steps(), output_centroid_silent_struct(), output_chi_stats(), output_constraints(), output_constraints_for_full_length(), output_distance_matrix(), output_general_base_pair_steps(), output_interface_graphviz(), output_local_minima(), output_minipose_coords_test(), output_native_ss_info(), output_residue_types(), output_sasa(), output_single_motif(), output_struct_type(), output_sugar_geometry_parameters(), output_sugar_internal_dof(), output_to_silent(), overlay_bb_bondangles(), apps::public1::scenarios::chemically_conjugated_docking.pack_extra_bodies(), pack_interface(), pack_it(), pack_o2prime(), pack_phosphates(), pack_polar_hydrogens(), pack_rotamers_test(), MinPackMin.pack_sidechains(), pack_sidechains(), packing_score(), packmin_unbound_pep(), pairE_test(), parse_nonstandard_angles(), parse_nonstandard_bondlengths(), HECTMover.parse_options(), parse_pathway_test(), parse_pdb_pos(), parse_resfile(), FixbbJobQueen.parse_sfxns_and_taskops(), parse_ss_regions(), ExposedStrandMover.parse_strand_ids(), pass_VDW_replusion_screen_fast(), pass_VDW_replusion_screen_slow(), pdb_little_motif_test(), pdb_scoring(), pdb_stats(), pdb_to_silent_file(), pdb_to_silent_file_simple(), pdbslice(), pdbstats_test(), pep_energies_analysis(), pep_phipsi_analysis(), pep_rmsd_analysis(), pep_scan_analysis(), peptide_plane_test(), peptide_plane_test_OLD(), perturb_and_rescore(), perturb_bb(), perturb_bb_and_relax(), UniformPerturber.perturb_chain(), perturb_pep_bb(), phosphate_stats(), ThisApplication.pick_frags(), myspace::Scheduler.pick_hashing_res(), apps::pilot::MultiTemplateAlignChunkMover.pick_random_chunk(), picking_test(), pid(), place_water_acceptor(), place_water_donor(), place_waters_and_minimize(), plot_scoreterm(), polar_pdbstats_from_pose(), polar_pdbstats_test(), pose2bin(), pose2frags(), InterfaceDDGBindJobInputter.pose_from_job(), pose_from_scratch(), myspace.pose_from_scratch(), HBondReporter.pose_name(), pose_nbratom_center_of_mass(), pose_pos_from_pdb_pos(), pose_resid_from_PDB(), pose_to_string(), poses_from_cmd_line(), poses_from_cmd_line_noPDBtag(), positions_incompatible_with_task(), possible_disulfide(), post_rebuild_bulge_assembly(), predict_AE(), predict_chem_map_test(), PhProtocol.prepack_pose(), Prepare(), prepare_full_length_start_model(), prepare_start_model(), prepare_threaded_model(), dsRNA_grow.prepend_Aform_residue(), CalcsTestMover.pretty_print(), MPInterfaceStatistics.print_aa_statistics(), print_all_torsions_test(), print_energies(), PhDocking.print_hbonds(), PhProtocol.print_hbonds(), print_hbonds_test(), print_internal_coord_test(), print_internal_coordinates(), print_pep_analysis(), MPDomainAssembly.print_score(), print_secstruct_test(), DesignGlycansProtocol.print_sequences(), ExposedStrandMover.print_sheets(), ExposedStrandMover.print_sheets_extras(), print_surface_score_by_res(), print_torsions_check(), print_tree(), printBondAngles(), protocols::abinitio::JumpSpecificAbrelax.process_decoy(), process_file_list(), process_for_motifs(), process_pose(), processRegions(), proclose_test(), ui::widgets::PoseEditor.progress_data_received(), proline_rama_pdbstats_from_pose(), protein_helix_test(), protein_motif_offset(), protocols_main(), put_constraints_on_helix(), pymol_struct_type_test(), quick_score_test(), rama2b_test(), BreadthMover.rama_apply(), rama_prepro_test(), rama_test(), myspace.ramp_repack_min(), randomly_open_pose_loop(), randomly_shift_and_tilt_pose(), rb_entropy_test(), rb_test(), RBSegmentRelax_test(), read_fold_tree_from_file(), read_in_extension(), read_in_flexible_regions(), read_in_mutations(), read_library_w_simpose(), read_native_pose(), read_native_sequence_for_entity_elements(), read_occupancy_data(), read_pose(), read_write(), real_test_GA(), ChallengeMover.realign(), reasonable_disulfide_orientation(), rebuild_centroid_test(), rebuild_test(), rebuild_trimmed_loops(), DisulfideBondEnergy.rebuildAndDetectDisulfideBond(), receive_silent_struct(), recenter_with_missing(), reconstruct_lattice_pose_info(), DockGlycansProtocol.record_pose_metrics(), myMC.recover_low(), zinc_stats::ZincStatisticGenerator.recursively_model_rotamer_chis(), refine(), refine_fa_pep_bb(), refine_pose(), refresh_cutpoints(), region_constraint_score(), region_density_score(), region_score(), rel_sasa_score(), protocols::abinitio::JumpSpecificAbrelax.relax(), PhProtocol.relax_pose(), apps::pilot::momeara::HBondConformation.relax_pose_around_hbond(), relax_test(), remove_all_virtual_residues(), remove_membrane_residue(), remove_pep_buffer_res(), remove_pep_res(), remove_pose_water(), reorder_foldtree(), reorient_to_base_pair_coordinate_system(), A3BHbsCreatorMover.repack(), HbondZinc.repack(), HbondZincBackbone.repack(), repack(), repack_all(), repack_iface(), repack_minimize_test(), repack_pose(), repack_test(), repackmin(), HemeReplace.replace_ligand(), replace_torsion_angles(), report(), GlycanClashCheckMover.report_data(), res2stub(), res_lvl_analysis(), res_type_score(), resample_full_model_test(), rescore(), rescore_test(), residue_distance(), restore_hack(), ui::widgets::PoseEditor.result_received(), retrieve_capri_data_from_pose(), abbinding.return_raw_scores(), reverse_doublet_test(), apps::pilot::SampleSecondaryStructureAlignmentMover.revert_loops_to_original(), PerturbStruct.revert_muations(), rg2d(), rhiju_pack(), rhiju_pdbstats(), MinPackMin.rigid_body_minimization(), DisulfEpos.rms(), DisulfEposDatabase.rms(), rmsd_compute(), rna_assemble_all_combinations_test(), rna_assemble_test(), rna_backbone_rebuild_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_chain_closure_test(), rna_close_chainbreaks_test(), rna_close_loop_test(), rna_denovo(), rna_denovo_legacy(), rna_design_gap_test(), rna_design_test(), rna_features_from_pose(), rna_fullatom_minimize_silent_test(), rna_fullatom_minimize_test(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), rna_helix_pdbstats_from_pose(), rna_idealize_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_motif_test(), rna_o2prime_test(), rna_protein_pdbstats_test(), rna_protein_prepack_test(), rna_protein_rb_test(), rna_protein_repack_test(), rna_resample_test(), rna_sample_virtual_sugar(), rna_sequence_recovery_metrics(), rna_stack_pdbstats_from_pose(), rna_stats_test(), rna_suitename(), rna_thread_test(), rna_torsion_check_test(), myMC.roll(), rot_pose(), rotamer_trials_test(), RotamerAnalysis(), rotamerize(), rotamerize_rna_test(), rotamerize_structure(), rotate_into_nucleobase_frame(), rots_from_pose(), rottrial_residue(), rottrialmin_residue(), protocols::abinitio::Application.run(), DockingBenchmark< dock, TScale >.run(), MinimizerBenchmark< sft, TScale >.run(), run(), run_3bpy(), myspace::Scheduler.run_combine(), run_diiron_glu(), run_hd(), run_hh(), myspace::Scheduler.run_LH(), myspace::Scheduler.run_LHeval(), run_m8(), myspace::Scheduler.run_md(), myspace::Scheduler.run_NM(), myspace::Scheduler.run_NM_evalmodes(), run_parallel_docking(), run_pep_prep(), run_sf4h(), run_test(), run_tests(), run_tyr_his(), run_zn2his(), RunPepSpec(), same_secondary_structure(), ChallengeMover.sample(), sample_new_base_in_two_base_pair_pose(), sample_rama_test(), sample_rna_dofs_new(), sample_state_to_state(), sample_torsions(), sample_trp_test(), sample_trp_tyr_test(), SamplingManager.SamplingManager(), sasa_bunsats(), sasa_separation(), sasa_test(), save_contact_info(), save_ss_info(), save_torsion_M_v(), save_torsions(), A3BHbsCreatorMover.scan(), myspace.scan_contact(), scan_energy(), scan_Evalue(), myspace::DataClass.scan_Evalue(), myspace.scan_Evalue(), myspace::DataClass.scan_Evalue_and_write(), scan_hbond_jumps(), scan_neutral(), scan_rotamer(), myspace::Scheduler.Scheduler(), scheme_score(), scmove_residue(), PairScore.score(), score12_plot_test(), score_and_minimize(), CapriTotalEnergy.score_experimental_constraints(), score_folded_residues(), score_loop(), score_loops(), score_pdb(), ZincSiteEvaluator.score_pose(), score_residue_pair(), score_rnp(), scoring_test(), screen_phosphates(), search_other_atoms(), search_translations(), select_loop_residues(), InterfaceDDGMover.separate_complex(), separation(), sequence_tolerance_main(), sequence_tolerance_mf_main(), SequenceCoords.SequenceCoords(), dsRNA_grow.set_Aform_torsions(), apps::pilot::AlignChunkMover.set_aligned_chunk(), set_all_loop_dihedrals_to_180(), set_chain_end_fold_tree(), set_disulf(), set_dof(), MinTestMover.set_foldtree_for_variable_movement(), set_fullatom_flag_test(), set_helix_torsions(), set_ideal_geometry(), apps::pilot::SampleSecondaryStructureAlignmentMover.set_loops_to_virt_ala(), set_pep_cst(), set_pep_csts(), UniformPerturber.set_pose_after_closure(), set_pose_conformation(), set_pose_occ_and_bfac(), MPDomainAssembly.set_random_torsion(), set_secstruct_from_psipred_ss2(), set_stub_transform_test(), set_up_covalent_connections(), HECTMover.set_up_foldtree(), set_up_termini(), SamplingManager.setup(), HPatchByChainNPDCalculator.setup(), NBuriedUnsatsCalcultor.setup(), CenRotDockingMover.setup(), zinc1_homodimer_design.setup(), zinc2_homodimer_design.setup(), setup_align_atom_map(), setup_atom_number(), setup_backbone_atoms(), setup_bonded_protein_rna_pose(), setup_CA_constraints(), setup_ca_constraints(), setup_capri_data(), setup_constraints(), setup_coord_csts(), setup_crazy_fold_tree(), setup_design_res(), setup_dinucleotide_pose(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_dock_foldtree(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_dock_low_res(), setup_double_helix_pose(), setup_favor_native(), abbinding.setup_foldtree(), PhDocking.setup_foldtree(), setup_for_folding(), setup_frags_from_vall(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_general_min_foldtree(), zinc2_homodimer_setup.setup_grafted_monomer(), setup_heavy_atoms(), setup_hotspot_filter(), setup_hydrophobic_cbetas(), BBG_Cyclic_Mover.setup_locker(), setup_loops_from_mapping(), CrystFFTDock.setup_maps(), zinc2_homodimer_design.setup_metalsite(), zinc1_homodimer_design.setup_metalsite(), zinc1_homodimer_design.setup_metalsite_constraints(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_minimizer(), CalcIrms.setup_native(), setup_one_chain_pose(), myspace.setup_packer(), setup_per_residue_rmsd_atom_map(), setup_pert_foldtree(), A3BHbsDockDesignMinimizeMover.setup_pert_foldtree(), DougsDockDesignMinimizeMagicMover.setup_pert_foldtree(), HotspotPlacementMover.setup_pert_foldtree(), HotspotPlacementMover.setup_pert_foldtree_byres(), PhDocking.setup_pH_mode(), setup_pose(), setup_pose_setup_class(), setup_pose_with_loop(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_relax(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_repack_cdrs(), setup_repeat_pose(), abbinding.setup_RepulsiveRampMover(), setup_rhiju_fold_tree(), setup_rmsd_atom_map(), CapriTotalEnergy.setup_rna_atoms_for_pose(), setup_rna_base_pair_constraints(), setup_rna_chainbreak_constraints(), setup_rna_minimizer(), zinc1_homodimer_design.setup_rollmoving(), setup_sam_constraints(), setup_sam_constraints_for_t033(), setup_secstruct_dssp(), apps::pilot::SampleSecondaryStructureAlignmentMover.setup_startree(), setup_symmetric_dimer(), setup_t469_zn_tether(), abbinding.setup_task_and_repack(), PhDocking.setup_task_and_repack(), HemeReplace.setup_task_factory(), SymFixbbMover.setup_task_mm(), zinc1_homodimer_design.setup_taskfactory(), zinc2_homodimer_design.setup_taskfactory_scorefunction_movers(), setup_two_base_pair_pose(), setup_two_base_pair_pose_with_chainbreak(), setup_VDW_rep_atom_map_list(), setup_zf_pose(), shear_moves_test(), sheffler_voids(), show_clashes(), show_dna_geometry(), show_intrachain_energies(), MembraneRelaxMover.show_membrane_position(), show_pairing_info(), show_protein_DNA_interactions(), show_residue_hbonds(), sicdock_thread_num(), sidechain_fastrelax(), sidechain_sample(), sidechain_sasa(), simple_centroid_test(), simple_copy_test(), simple_dna_test(), simple_frag_test(), simple_hbond_test(), simple_loop_modeling_test(), simple_minimization(), simple_opte_test(), simple_packing(), simple_relax(), simple_rotamer_recovery(), simple_rotamer_test(), BuriedUnsatPolarsFinder.single_bunsat_thorough_check(), single_position_motif_scan(), single_res_task(), single_sasa_calc(), slice_ellipsoid_envelope(), slice_pdb(), slice_sample_res_and_surrounding(), CenRotDockingMover.slide_into_contact(), apps::pilot::HelixMover.slide_non_ideal_helix(), slidearound(), slow_clash(), slow_nbcount(), slow_nbset(), small_min_test(), small_moves_test(), soft_pack(), spanfile_for_each_chain(), spanfile_from_pdb(), spec_test(), sphere_cen_nc_calculator(), sphere_FA_nc_anyatom_calculator(), sphere_FA_nc_calculator(), SphereGrinder(), spinner_test(), split_chains(), split_fa_dun(), split_pdb_into_ss_chunks(), ss_test(), apps::pilot::AlignChunkMover.steal_torsion_from_template(), stepwise_lores_test(), stepwise_monte_carlo_legacy(), stepwise_template_test(), myspace::Evaluator.store_gdt0(), storeposedata(), string_to_pose(), strip_termini(), HubDenovo.stupid_ddg(), sugar_frag_RNA_test(), sugar_geometry_RNA_test(), superimpose_pdb(), superimpose_tmalign(), swa_rna_sample(), sweep_params_from_match_constraint_file(), switch_to_cen(), switch_to_fa(), HDdesignMover.sym_repack_minimize(), SymmDataTest(), SymRBMover.SymRBMover(), DisulfideBondEnergy.tabulate(), GlycanClashCheckMover.tabulate_individual_data(), tag_from_pose(), tar_motif_test(), target_constraints(), HDdesignMover.task_constraint_setup(), test(), test_actcoord(), myspace.test_bbgauss(), myspace::GraftTester.test_cart_graft(), test_chunk(), test_ddg(), test_deriv_pose(), test_dunbrack_io(), test_function(), test_gb(), test_gradient(), test_kc(), test_kc2(), test_known_value(), test_lh_counts(), myspace.test_loophash(), myspace.test_MD(), test_membrane_chain(), test_membrane_conformation(), test_membrane_fold_tree(), TestJD2Mover.test_move(), protocols::moves::FragCaptureMover.test_move(), Benchmark.test_move(), RamaTestMover.test_move(), ScTrials.test_move(), Minimize.test_move(), ExemplarMover.test_move(), NCMinimize.test_move(), protocols::moves::SimpleCstMover.test_move(), test_NM(), test_NMmin(), myspace.test_NMrelaxer(), test_NMrelaxer(), test_protein_rna(), test_rama(), myspace::GraftTester.test_rb_min_graft(), myspace.test_recombine(), myspace.test_relax(), test_replicate_xform(), InterfaceFeaturesTests.test_reporter(), test_scorefxn_io(), test_suck_res(), test_vs_dots(), tf_specificity_test(), thermal_sampler(), thread_fxn(), PhProtocol.titrate_pH(), tm_superimpose(), torsion2big_bin_string(), torsion2decoy(), torsion2pdb(), TorsionList.TorsionList(), trans_pose(), CrystFFTDock.transform_pdb(), CrystCluster.transform_pdb(), transform_pose(), apps::pilot::SampleSecondaryStructureAlignmentMover.translate_virt_to_CoM(), transmit_silent_struct(), trim_back_t033_pose(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), trim_pdb(), trim_pose_termini(), two_base_pairs_test(), two_base_pairs_via_loop_closure_test(), TwoChainInterface.TwoChainInterface(), twoChainPose(), TwoChainTenANeighbors.TwoChainTenANeighbors(), tyr_ct(), HECTMover.ubq_constraints(), apps::public1::scenarios::chemically_conjugated_docking.ubq_ras_distance(), apps::public1::scenarios::chemically_conjugated_docking.ubq_ras_rotation_angle(), unbound_protein_minimization(), BreadthMover.uniform_apply(), unsatisfied_buried_polars(), unvirtualize_phosphates(), up_jump_tree(), SamplingManager.update(), update_bicelle_radius(), update_double_vesicle(), CovalentPeptidomimeticDockDesign.update_hydrogens(), CovalentPeptidomimeticCreator.update_hydrogens(), update_vesicle_radius(), use_backrub(), varsoldist_rotamer_dots_for_pose(), vary_bond_length(), vary_geometry_backbone(), vary_geometry_RNA(), vary_geometry_sidechains(), vdw_stats(), vlb_test(), vMPI_Bcastpose(), vMPI_transmitpose(), vsasa_bunsats(), water_test(), water_test_fixed_O(), wriggle_test(), protocols::moves::SimpleCstMover.write(), PBPotentialMover.write_APBS_config(), write_base_pair_step_to_silent_struct(), write_buns_and_dots_kinemage(), write_cluster_frags(), write_hbgeoms_to_database(), XMLprinterMover.write_output_file(), write_respair_scores_to_database(), write_scores_and_hbond_geoms_to_database(), xform_pose(), xform_pose_rev(), zero_occ_for_deleted_atoms(), zf_chainbreak_distance(), zf_relax_test(), zf_test(), zif268_test(), and ZincMinimize.zn_min_pack().
