Here is a list of all file members with links to the files they belong to:

- a -

• a : T17.anonymous.hpp
• 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
• aa : gen_env_dep_orient.m , smooth_2D.m , gen_env_dep_orient_draw.m
• aa2index() : pep_opt.cc , pep_opt_parallel.cc , pep_prepspec.cc , pep_spec.06-23.cc , pep_spec.cc , pep_spec_flx.cc , pep_spec_flx.mov.cc , pepspec.cc
• aa2sim_all() : cluster_hotspot_docking.cc
• aa2sim_ca() : cluster_hotspot_docking.cc
• aa2sim_sc() : cluster_hotspot_docking.cc
• aa_aa : draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_pair_decompose.m
• aa_aa_th1 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m
• aa_aa_th2 : gen_env_dep_orient_draw.m , gen_env_dep_orient.m
• aa_all : draw_gen_env_dep_pair.m , gen_env_dep_pair.m
• aa_core : draw_gen_env_dep_pair.m , gen_env_dep_orient_draw.m , gen_env_dep_pair.m , draw_gen_env_dep_pair.m , gen_env_dep_pair.m
• aa_core_da1() : gen_env_dep_orient.m
• aa_core_da2() : gen_env_dep_orient.m
• aa_core_dat_r_ang : gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• aa_core_p_r_ang : gen_env_dep_orient.m , gen_env_dep_orient_draw.m , gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• aa_core_sum_r : gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• aa_surf : draw_gen_env_dep_pair.m , gen_env_dep_orient_draw.m , gen_env_dep_pair.m
• aa_surf_da1 : gen_env_dep_orient.m
• aa_surf_da2() : gen_env_dep_orient.m
• aa_surf_dat_r_ang : gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• aa_surf_p_r_ang : gen_env_dep_orient.m , gen_env_dep_orient_draw.m , gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• aa_surf_sum_r : gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• aacore_core_da1 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• aacore_core_da2() : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m
• aacore_surf_da1 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• aacore_surf_da2 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• aandx : gen_vdw_radius.m , gen_vdw_radius_soft.m
• aasurf_core_da1 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m
• aasurf_core_da2 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• aasurf_surf_da1 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• aasurf_surf_da2 : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• abbindingOP : ab_binding.cc
• AbInitio_MPIOP : AbInitio_MPI.cc
• absfpart() : spacegroup.hh
• absorb_surrounded_canonicals() : rna_test.cc
• acc_store_hbs() : cnl_env_lost_hbs.cc
• accept_new_weight_set() : optE_test.cc
• accum_hbdon_shoene() : tgtres_polar_sho_energies.cc
• actual_disulfide() : disulfides.hh
• add() : T20.template.hpp
• add_agc() : smhybrid.cc , organopv.cc , coiled_coil.cc , coiled_coil_zn.cc
• add_apc() : coiled_coil.cc , coiled_coil_zn.cc , organopv.cc , smhybrid.cc , bpy.cc
• add_chi_tags() : stepwise_test.cc
• add_constraints() : vancomycin.cc , homolog_cst.hh
• add_coordinate_constraints() : rna_test.cc
• add_crystinfo_to_pose() : cryst_design.cc
• add_Cu_chains() : fit_helixparams.cc
• add_deviations() : avrg_silent.cc
• add_dhc() : coiled_coil_zn.cc , coiled_coil.cc
• add_dna_states() : multistate_design_ga.cc
• add_fa_cst() : coiled_coil.cc , coiled_coil_zn.cc
• add_fnr_constraints() : minimization_test.cc , msd.cc
• add_histograms_together() : generate_orbital_statistics.cc
• add_lig_cst() : coiled_coil_zn.cc
• add_my_options() : repeat_demo.cc
• add_pep_buffer_res() : pep_gly.cc , pep_prepspec.cc
• add_pep_res() : pep_spec.06-23.cc , pepspec.cc , pep_spec_flx.cc , pep_spec.cc , pep_spec_flx.mov.cc
• add_protocols() : reverse_conversion_util.hh
• add_regular_scores_to_scorefile : InterfaceAnalyzer.cc
• add_rosetta_options_0() : option.cc.gen.hh
• add_scores() : whitney_identify_epitope.cc
• add_shell() : mpframework_test2.cc
• add_side_chains_partialthread() : tj_util.hh
• add_symm_sf4() : coiled_coil.cc
• add_symm_zns() : coiled_coil_zn.cc
• add_termini() : pep_prepspec.cc , pepspec.cc , pep_spec_flx.mov.cc , pep_spec_flx.cc , pep_spec.cc , pep_spec.06-23.cc
• add_triazole_constraints() : mike_linker_test.cc
• add_user_constraints() : bettercluster.cc , design_cycpeptide_MPI.cc
• add_virtual_res() : rna_pdb_scoring.cc , adenosine_stack_test.cc
• add_vrts() : membrane_foldtree.cc , membrane_foldtree2.cc
• addcc() : coiled_coil.cc , coiled_coil_zn.cc , match_disulf.cc
• addcyclicconstraints() : bettercluster.cc , design_cycpeptide_MPI.cc
• addvv() : gpu_mat_vec.hh
• adesign() : atom_design.cc
• AdjacencyIter : undirected_graph.cc
• AdjacencyIterPair : undirected_graph.cc
• adjust_pose_chi() : turner_rules_test.cc
• adjust_ref_weights() : cryst_design.cc
• advance_to() : format.h
• AE : SID_rescore.cc
• AHD_cutoff : BuriedUnsatPolarsFinder2.cc
• AHD_opkey : sasa_buns.cc , vsasa_pdbcode_res.cc
• AHdist_opkey : sasa_buns.cc , vsasa_pdbcode_res.cc
• AICS : gensym_3bpy_from_dimer.cc
• AID : flail.cc
• aidr_as_float() : gpu_bit_utils.hh
• AIDs : motif_denovo_hb.cc , motif_hash_util.cc
• aj : draw_gen_env_dep_orient_decompose.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , draw_matrix.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , gen_env_dep_orient.m
• ALA : load_pair_env_table.m , gen_vdw_radius.m , load_angle_r_table.m , gen_env_dep_orient_decompose.m , load_pair_env_table_ref.m , load_pair_env_table.m , cal_env.m , draw_matrix.m , draw_gen_env_dep_orient_decompose.m
• ala_ct() : evalFullLength.cc , evalRepeats.cc
• alapose() : FunGroupTK.cc , IKFGDB.cc
• align_backbone_by_chunk() : challenge.cc
• align_carboxyl_diiron() : genmatch.cc
• align_carboxyl_diiron_OLD() : genmatch.cc
• align_carboxyl_m8() : genmatch_m8.cc
• align_conformations() : make_retroinverso.cc
• align_helix() : fit_helix_in_map.cc
• align_native_state() : CXdock.cc , sicdock.cc , dxdock_movie.cc
• align_pdbs() : swa_rna_util.cc
• align_pdbs_function() : parin_test.cc
• align_pose() : align_substructure.cc
• align_pose_general() : swa_rna_util.cc
• align_poses() : make_a3b_bundle.cc , make_betahelicalbundle.cc , make_helicalbundle.cc
• align_sf4() : coiled_coil.cc
• align_t : format.h
• align_with_offset() : bettercluster.cc
• align_zns() : coiled_coil_zn.cc
• alignaxis() : symdock_enum.cc , symdock_enum_3_1.cc , matdes_design_2comp.cc
• alignhelix() : helix_assembly.cc
• alignment_atoms_in_res() : bettercluster.cc
• alignment_torsions_in_res() : bettercluster.cc
• all : calc_pair_matrix.m
• all_pair_energies() : per_residue_energies.cc
• all_pose_residues() : erraser2.cc
• allifnone() : IKFGDB.cc , FunGroupTK.cc
• ALLOWED_DOFS : plot_scoreterm.cc
• aln : minimalCstRelax.cc
• alncys() : sf4_hash.cc
• alpha : pre_fill_dfire.m , pre_fill_dfire_2D.m
• alpha_to_beta() : a3b_hbs_creator.cc
• already_minimized() : minimize_with_cst.cc
• analyze_base_pair_test() : analyze_base_pairing.cc
• analyze_interface_test() : dna_spec_test.cc , simple_dna_regression_test.cc
• analyze_poses_for_convergence() : erraser2.cc
• AnchorFinderMoverOP : AnchorFinder.cc
• angle_degrees() : symdock_enum.cc , symdock_enum_3_1.cc
• ANGLE_DELTA : topo_driver.cc
• angle_diff() : get_dihedral_b3aa.cc , get_dihedral_peptide.cc , get_dihedral_peptoid.cc , peptoid_rotamer_prediction_benchmark.cc
• angle_rotation_increment : zinc2_homodimer_setup.cc
• anglestats_local() : angle_stats.cc
• annealTemperature() : flexibleLoopDesign.cc
• AnnotatedFragDataCOP : reportFragments.cc
• AnnotatedFragDataOP : reportFragments.cc
• AOCT : gen_xtal_dimer_from_trimer.cc , gensym_3bpy_from_dimer.cc , genI213_nocontacts.cc
• APDBCMoverOP : AnchoredPDBCreator.cc
• append_alanines() : design_truecycpeptide_fromstub.cc
• append_fold_tree_to_file() : backrub_pilot.cc
• append_jumpless_pose() : smhybrid.cc
• append_pose_by_jump() : domain_assemble.cc , design_truecycpeptide_fromstub.cc
• append_sequence_to_pose() : BuildFloppyTail.cc
• apply_all() : turner_two_chain.cc
• apply_all_frags() : stepwise_centroid_test.cc
• apply_angle_set() : coarse_rna_test.cc
• apply_backbone() : turner_two_chain.cc
• apply_backbone_rotamer() : rna_test.cc
• apply_filter_base_stack_direction() : turner_rules_test.cc
• apply_ideal_A_form_torsions() : turner_rules_test.cc
• apply_linked_constraints() : minimization_test.cc , msd.cc
• apply_mask() : easy_target_test.cc
• apply_nucleoside() : turner_two_chain.cc
• apply_nucleoside_torsion() : turner_test_one_chain.cc
• apply_rigid_body_settings() : turner_two_chain.cc , turner_test_double_helix.cc
• apply_rotation() : mammoth_hack.cc
• apply_south_syn_to_dinucleotide_pose() : turner_rules_test.cc
• apply_suite_torsion() : turner_test_one_chain.cc
• apply_suite_torsions() : turner_test_double_helix.cc , turner_rules_test.cc
• apply_torsion_set() : lariat_modeling.cc
• apply_transform() : pdb_gen_cryst.cc , challenge.cc
• apps_pilot_rayyrw_closability_score_hh : closability_score.hh
• apps_pilot_rayyrw_min_pack_min_hh : min_pack_min.hh
• apps_pilot_rayyrw_overlap_score_hh : overlap_score.hh
• apps_pilot_rayyrw_rms_util_hh : rms_util.hh
• apps_pilot_rayyrw_util_hh : util.hh
• ar : smooth_2D.m
• aramid_main() : aramid_folding.cc
• ArchCOP : tcdock.cc
• ArchOP : tcdock.cc
• ARG : gen_vdw_radius.m , load_pair_env_table.m , load_angle_r_table.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , load_pair_env_table.m , load_pair_env_table_ref.m
• arg() : core.h
• ARG : draw_gen_env_dep_orient_decompose.m , draw_gen_env_dep_pair.m , draw_matrix.m , cal_env.m , draw_gen_env_dep_pair_decompose.m
• argmax() : mkresfile_i213.cc
• argv : cenrot_jd2.cc , calibur.cc
• aro_pack_output() : pdbstats_test.cc
• aro_pack_pdbstats_from_pose() : pdbstats_test.cc
• array2vecs() : gpu_linker.cc
• ASN : gen_env_dep_orient.m , gen_vdw_radius.m , load_pair_env_table.m , load_angle_r_table.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , load_pair_env_table_ref.m , load_pair_env_table.m , cal_env.m , draw_matrix.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_orient_decompose.m
• ASP : draw_gen_env_dep_orient_decompose.m , gen_vdw_radius.m , load_pair_env_table.m , load_angle_r_table.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , load_pair_env_table_ref.m , load_pair_env_table.m , cal_env.m , draw_matrix.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , gen_env_dep_orient.m
• ASP1 : hczndimer.cc
• ASP2 : hczndimer.cc
• ASP3 : hczndimer.cc
• asp_bb2m() : gpu_xforms.hh
• aspd_bb2m() : gpu_xforms.hh
• aspd_m2bb() : gpu_xforms.hh
• aspe_bb2m() : gpu_xforms.hh
• aspe_m2bb() : gpu_xforms.hh
• ASSERT_ONLY : assert.hh
• assign_models() : kcluster.cc
• assign_rigid_body_settings_to_clusters_test() : turner_rules_test.cc
• assign_stack_faces() : turner_rules_test.cc
• assign_tag() : create_hierarchy.cc
• assure() : gen_apo_grids.cc , gen_lig_grids.cc
• ATET : gen_xtal_dimer_from_trimer.cc , genI213_nocontacts.cc , gensym_3bpy_from_dimer.cc
• atom1_vector : extract_motifs.cc
• atom2_vector : extract_motifs.cc
• atom3_vector : extract_motifs.cc
• atom_line() : dna_spec_test.cc , simple_dna_regression_test.cc , dna_dr_test.cc
• atom_tree_torsion_test() : test1.cc
• atom_types_test() : test1.cc
• atom_vdw_test() : dna_spec_test.cc , simple_dna_regression_test.cc
• atoms : gpu_octree_impl_test.cc
• atoms_have_bond_to_bonded_atoms() : erraser2.cc
• atoms_have_mutual_bond_to_atom() : erraser2.cc
• attach_abego_pools() : quotapicker_demo.cc
• attach_simple_abego_pools() : quotapicker_demo.cc
• automorph_rmsd() : rmsd_calculator.cc
• average() : ddg_benchmark.cc , pepspec_anchor_dock.cc , monomer_ddg.cc , pep_prep.cc , pepspec_anchor_dock.cc
• average_degree() : cxdesign.cc , matdes_design.cc , matdes_design_2comp.cc , matdes_mutalyze.cc , pentcb_design.cc , rescore_i213.cc , will_mutalyze.cc
• average_score_components() : ddg_benchmark.cc , monomer_ddg.cc
• avg_ca_position() : evalRepeats.cc , findNaturallyOccuringAlphaRepeats.cc , armEval.cc
• axis : ZincMinimize.cc , ZincSiteEvaluator.cc , ZincMatchFilter.cc , zinc1_homodimer_design.cc , zinc1_homodimer_setup.cc , zinc2_homodimer_design.cc , zinc2_homodimer_setup.cc , draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
• axis_angle() : cryst_gen.cc