- a -

• aa2idx() : core::scoring::saxs
• aa2name() : core::chemical
• aa2oneletter() : core::chemical
• aa_from_name() : core::chemical
• aa_from_oneletter_code() : core::chemical
• abego_index() : protocols::frag_picker::quota
• ACETYLATED_NTERMINUS() : core::chemical
• ACETYLATION() : core::chemical
• add_atom() : core::kinematics
• add_atom_type_set_parameters_from_command_line() : core::chemical
• add_chainbreaks_according_to_jumps() : protocols::toolbox::pose_manipulation
• add_claims_from_file() : protocols::topology_broker
• add_claims_from_stream() : protocols::topology_broker
• add_cmdline_claims() : protocols::topology_broker
• add_comment() : core::pose
• add_conformation_viewer() : protocols::viewer
• add_constraint_to_residue_constraints() : core::scoring::constraints
• add_constraints_from_cmdline() : core::scoring::constraints
• add_constraints_from_cmdline_to_pose() : core::scoring::constraints
• add_constraints_from_cmdline_to_scorefxn() : core::scoring::constraints
• add_constraints_from_file() : protocols::dna
• add_coordinate_constraints() : core::scoring::constraints , protocols::protein_interface_design::movers , protocols::seeded_abinitio
• add_coordinate_constraints_to_pose() : protocols::loops , protocols::relax
• add_cutpoint_variants() : protocols::loops , core::util , protocols::forge::methods
• add_dens_scores_from_cmdline_to_scorefxn() : core::scoring::electron_density
• add_dist_constraints() : protocols::seeded_abinitio
• add_edges() : protocols::forge::methods
• add_fa_constraints_from_cmdline() : core::scoring::constraints
• add_fa_constraints_from_cmdline_to_pose() : core::scoring::constraints
• add_fa_constraints_from_cmdline_to_scorefxn() : core::scoring::constraints
• Add_harmonic_chainbreak_constraint() : protocols::swa::rna
• add_hbs_constraint() : protocols::simple_moves::hbs
• add_hydrogen_tracer() : protocols::ligand_docking
• add_hydrogens_tracer() : protocols::ligand_docking
• add_job_data_to_ss() : protocols::jd2
• add_ligand_conditionally() : protocols::ligand_docking
• add_loop() : protocols::loops
• add_loop_flank_residues_bb_to_movemap() : protocols::loops
• add_lower_terminus_type_to_conformation_residue() : core::conformation
• add_lower_terminus_type_to_pose_residue() : core::pose
• add_monte_carlo_silent_viewer() : protocols::viewer
• add_monte_carlo_viewer() : protocols::viewer
• add_motif_bb_constraints() : protocols::motifs
• add_motif_sc_constraints() : protocols::motifs
• add_non_protein_cst() : protocols::hybridization
• add_oop_constraint() : protocols::simple_moves::oop
• add_relevant_restypes_to_subset() : protocols::toolbox::match_enzdes_util
• add_rna_chi_rotamers() : core::pack::rotamer_set
• add_score_line_string() : core::pose
• add_single_cutpoint_variant() : protocols::loops
• add_strand_pairs_cst() : protocols::hybridization
• add_to_individual_sol_energies() : core::scoring::geometric_solvation
• add_upper_terminus_type_to_conformation_residue() : core::conformation
• add_upper_terminus_type_to_pose_residue() : core::pose
• add_variant_type_to_conformation_residue() : core::conformation
• add_variant_type_to_pose_residue() : core::pose
• add_variant_type_to_residue() : core::pose
• add_vec() : protocols::toolbox
• add_vertex() : protocols::forge::methods
• Add_virtual_O2Star_hydrogen() : protocols::swa::rna
• add_virtual_residue_to_cterm() : protocols::relax
• AddPyMolObserver() : protocols::moves
• addScoresForLoopParts() : protocols::loops
• ADDUCT() : core::chemical
• addVirtualResAsRoot() : core::pose
• adjust_des_residues() : protocols::seeded_abinitio
• adjust_mm_to_length() : protocols::seeded_abinitio
• adjust_residues() : protocols::seeded_abinitio
• adjust_single_residues() : protocols::seeded_abinitio
• advance_euler_angles() : protocols::match
• advance_to_neighbor_bin() : protocols::match
• alapose() : protocols::kinmatch
• align_naive() : core::sequence
• align_poses() : protocols::swa::rna
• align_poses_naive() : core::sequence
• align_RG() : core::sequence
• align_to_native() : protocols::antibody2
• alignment_from_cmd_line() : protocols::comparative_modeling
• alignment_from_pose() : core::sequence
• alignment_into_pose() : core::sequence
• alignment_probabilities() : protocols::medal
• alignments_from_cmd_line() : protocols::comparative_modeling
• all_atom_rmsd() : core::scoring
• all_visited() : core::graph
• allifnone() : protocols::kinmatch
• allocate_matrix() : protocols::frag_picker::scores
• Analyze_base_bin_map() : protocols::swa::rna
• ANCHOR_TARGET() : protocols::anchored_design
• angle_between() : protocols::rigid
• angle_diff() : protocols::MakeRotLib
• angles() : core::scoring::packstat::old , core::scoring
• annotated_atom_graph_from_conformation() : core::conformation
• annotated_to_oneletter_sequence() : core::pose
• any_atoms_within_cutoff() : core::pack::task::operation::util
• append_automorphic_rmsd() : protocols::ligand_docking
• append_interface_deltas() : protocols::ligand_docking
• append_ligand_grid_scores() : protocols::ligand_docking
• append_ligand_RMSD() : protocols::ligand_docking
• append_ligand_travel() : protocols::ligand_docking
• append_multi_residue_ligand_RMSD() : protocols::ligand_docking
• append_radius_of_gyration() : protocols::ligand_docking
• append_rsd_by_jump_near_atom() : protocols::toolbox::pose_metric_calculators
• apply_adducts_to_residue() : core::chemical
• apply_best_scoring_fragdata() : core::fragment
• apply_full_to_sub_mapping() : protocols::swa::rna
• apply_ideal_c2endo_sugar_coords() : core::scoring::rna
• apply_ideal_coordinates_for_alternative_pucker() : protocols::simple_moves
• apply_lk_ball_fraction_weight_for_hbonds() : core::scoring::methods
• apply_non_main_chain_sugar_coords() : core::scoring::rna
• apply_protonated_H1_adenosine_variant_type() : protocols::swa::rna
• apply_rotamer() : protocols::swa::rna
• apply_rotate() : protocols::ligand_docking
• apply_sequence_mapping() : protocols::loops
• apply_sub_to_full_mapping() : protocols::swa::rna
• apply_transformation() : protocols::hybridization
• apply_virtual_rna_residue_variant_type() : protocols::swa::rna
• are_seqs_different() : protocols::vip
• argrot_dna_dis2() : protocols::dna
• as_set() : protocols::medal
• asp_corrections() : protocols::MakeRotLib
• assemble_remark_line() : protocols::toolbox::match_enzdes_util
• assert_can_append() : protocols::swa::rna
• assert_can_prepend() : protocols::swa::rna
• assert_phosphate_nomenclature_matches_mini() : protocols::rna
• assign_abase_derivs() : core::scoring::hbonds
• assign_random_continuous_rotamer() : core::pack
• assign_random_rotamers() : core::pack
• assign_ss_dssp() : protocols::jumping
• at() : core::io::serialization
• atom_graph_from_conformation() : core::conformation
• atom_id_from_icoor_line() : core::chemical
• atom_id_to_named_atom_id() : core::pose , core::conformation
• atom_is_acceptor() : protocols::rna
• atom_is_aro() : core::scoring::hackelec
• atom_is_aro2() : core::scoring::hackelec
• atom_is_polar() : protocols::rna
• atom_map_valid_size() : protocols::hybridization
• atom_specific_rms() : protocols::motifs
• atom_square_deviation() : protocols::swa::rna
• atom_tracer() : protocols::ligand_docking
• atom_tree_dfunc() : core::optimization::symmetry , core::optimization
• atom_tree_get_atompairE_deriv() : core::optimization , core::optimization::symmetry
• atoms_interact() : core::scoring::methods
• attach_debugger() : protocols::optimize_weights
• automorphic_rmsd() : core::scoring
• avg_ca_position() : protocols::nonlocal
• avg_cluster_cen_dist() : protocols::MakeRotLib