- a -

• a() : core::pose::motif
• aa2idx() : core::scoring::saxs
• aa2name() : core::chemical
• aa2oneletter() : core::chemical
• aa2randomCodon() : core::chemical::NucleotideTools
• aa_from_name() : core::chemical
• aa_from_one_or_three() : core::chemical
• aa_from_oneletter_code() : core::chemical
• aa_trustworthiness() : core::scoring::motif
• abego3aa_to_index() : core::scoring
• abego_index() : protocols::frag_picker::quota
• abego_str() : protocols::denovo_design
• abego_to_index() : core::scoring
• abego_vector() : protocols::denovo_design
• absfpart() : protocols::cryst
• absolute_vec() : protocols::features::strand_assembly
• accumulate_bur_rotamer_oversats() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• accumulate_seqpos_oversats() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• add() : protocols::mean_field
• add_a3b_hbs_constraint() : core::pose::ncbb
• add_another_virtual_res() : protocols::toolbox::sample_around
• add_anti_chi_constraints() : core::pose::rna
• add_atom() : core::kinematics
• add_atom_type_set_parameters_from_command_line() : core::chemical
• add_atom_types_from_command_line() : core::chemical
• add_attributes_for_common_options() : protocols::ncbb
• add_attributes_for_helix_params() : protocols::helical_bundle
• add_attributes_for_make_bundle_minorhelix_defaults() : protocols::helical_bundle
• add_attributes_for_make_bundle_other_defaults() : protocols::helical_bundle
• add_attributes_for_make_bundle_symmetry() : protocols::helical_bundle
• add_attributes_for_minor_helix_params() : protocols::helical_bundle
• add_attributes_for_other_helix_params() : protocols::helical_bundle
• add_block_stack_variants() : core::import_pose
• add_bond_information() : core::io::mmtf
• add_bonds_to_sd() : core::io::mmtf
• add_chain_from_pose() : protocols::denovo_design
• add_chainbreaks_according_to_jumps() : protocols::toolbox::pose_manipulation
• add_chi_constraints() : core::pose::rna
• add_claims_from_file() : protocols::topology_broker
• add_claims_from_stream() : protocols::topology_broker
• add_clashes_to_shell() : core::pack::task::residue_selector
• add_cluster_comments_to_pose() : protocols::antibody::clusters
• 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() : protocols::hybridization
• 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_constraints_to_metal() : core::util
• add_coordinate_constraint_func_atoms() : protocols::relax
• add_coordinate_constraints() : core::scoring::constraints , protocols::protein_interface_design::movers , protocols::seeded_abinitio
• add_coordinate_constraints_to_pose() : protocols::loops , protocols::relax
• add_covalent_linkage() : core::util
• add_covalent_linkage_helper() : core::util
• add_covalent_linkages_to_metal() : core::util
• add_current_job_data_to_ss() : protocols::jd2
• add_custom_variant_type_to_pose_residue() : core::pose
• add_cutpoint_closed() : core::import_pose
• add_cutpoint_variants() : protocols::forge::methods , protocols::loops
• add_cutpoint_variants_for_ccd() : protocols::grafting
• add_cutpoints() : protocols::denovo_design
• add_dens_scores_from_cmdline_to_scorefxn() : core::scoring::electron_density
• add_dist_constraints() : protocols::seeded_abinitio
• add_edges() : protocols::forge::methods
• add_extra_bodies() : protocols::chemically_conjugated_docking
• add_extra_data() : core::io::mmtf
• 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_fade_chain_break_constraint_across_gap() : protocols::stepwise::modeler::rna
• add_generic_hbs_constraint() : core::pose::ncbb
• add_glycan_links_to_map() : core::io
• add_harmonic_chain_break_constraint() : protocols::stepwise::modeler::rna
• add_harmonic_dihedral_cst_general() : protocols::antibody::constraints
• add_hbs_constraint() : core::pose::ncbb
• add_hydrogen_tracer() : protocols::ligand_docking
• add_hydrogens_tracer() : protocols::ligand_docking
• add_if_not_empty() : core::io::mmtf
• add_init_dev_penalty() : protocols::mpi_refinement
• add_job_data_to_ss() : protocols::jd2
• add_ligand_conditionally() : protocols::ligand_docking
• add_link_and_ss_information() : core::io::mmtf
• add_linker_segments() : protocols::legacy_sewing
• add_loop() : protocols::loops
• add_loop_flank_residues_bb_to_movemap() : protocols::loops
• add_loops_from_bool_vector() : protocols::antibody::design
• add_lower_terminus_type_to_conformation_residue() : core::conformation
• add_lower_terminus_type_to_pose_residue() : core::pose
• add_mm_atom_type_set_parameters_from_command_line() : core::chemical
• add_monte_carlo_viewer() : protocols::viewer
• add_motif_bb_constraints() : protocols::motifs
• add_motif_sc_constraints() : protocols::motifs
• add_movemap_from_loopres() : protocols::mpi_refinement
• add_mutant_to_vectors() : protocols::relax::membrane
• add_network_resids_to_pose() : protocols::hbnet
• add_new_sequence_into_global_sequence() : core::pose::full_model_info
• add_non_protein_cst() : protocols::hybridization
• add_num_neighbors() : protocols::legacy_sewing
• add_number_base_pairs() : core::pose::rna
• add_number_native_base_pairs() : core::pose::rna
• add_oop_constraint() : core::pose::ncbb
• add_overlap_to_loops() : protocols::denovo_design::movers
• add_paired_residues() : protocols::denovo_design::components
• add_per_residue_simple_metric_schema() : core::simple_metrics
• add_poseinfo_to_ss() : protocols::mpi_refinement
• add_relevant_restypes_to_subset() : protocols::toolbox::match_enzdes_util
• add_remark() : protocols::denovo_design
• add_residue_selectors_to_datamap() : protocols::jd3
• add_residues_to_pose() : protocols::denovo_design
• add_reslabels_to_pose() : protocols::hbnet
• add_rna_chi_rotamers() : core::pack::rotamer_set
• add_rotamers_to_pose() : core::pack::interaction_graph
• add_score_line_string() : core::pose
• add_segment() : protocols::denovo_design::components
• add_segments_for_chain() : protocols::denovo_design::components
• add_shell() : core::membrane
• add_single_cutpoint_variant() : protocols::loops
• add_single_magnesium() : protocols::magnesium
• add_strand_pairs_cst() : protocols::hybridization
• add_string_real_pair_to_current_job() : protocols::jd2
• add_string_string_pair_to_current_job() : protocols::jd2
• add_string_to_current_job() : protocols::jd2
• add_strings_to_current_job() : protocols::jd2
• add_subelement_for_constraint_combination() : protocols::toolbox::match_enzdes_util
• add_subelement_for_parse_stub_sets() : protocols::protein_interface_design::movers
• add_syn_anti_chi_constraints() : core::pose::rna
• add_syn_chi_constraints() : core::pose::rna
• add_terminus_variants() : protocols::denovo_design::components
• add_ters_via_bonds() : core::io::mmtf
• add_these() : protocols::stepwise::modeler
• add_to_individual_sol_energies() : core::scoring::geometric_solvation
• add_to_list() : protocols::denovo_design
• add_to_multimodel_pdb() : core::io::pdb
• add_to_onebody() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• add_to_pose() : protocols::denovo_design::components
• add_to_pose_list() : protocols::stepwise::modeler
• add_to_twobody() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• add_triazole_constraint() : core::pose::ncbb
• add_upper_terminus_type_to_conformation_residue() : core::conformation
• add_upper_terminus_type_to_pose_residue() : core::pose
• add_vall_cheating_fragments() : protocols::frags
• add_vall_fragments() : protocols::frags
• add_values_from_center() : core::chemical::rna
• add_variant() : protocols::environment
• 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_O2Prime_hydrogen() : core::pose::rna
• add_virtual_res() : protocols::toolbox::sample_around
• add_virtual_residue_to_cterm() : protocols::relax
• add_virtual_sugar_res() : core::import_pose
• add_water_overcoordinated_hb_score() : protocols::hydrate
• add_whitespaces() : core::scoring::rna::chemical_shift
• add_xbond_information() : core::io::mmtf
• AddPyMOLObserver() : protocols::moves
• AddPyMOLObserver_to_conformation() : protocols::moves
• AddPyMOLObserver_to_energies() : protocols::moves
• addScoresForLoopParts() : protocols::loops
• AddUIObserver() : protocols::network
• AddUIObserver_to_conformation() : protocols::network
• AddUIObserver_to_energies() : protocols::network
• addVirtualResAsRoot() : core::pose
• AdjacentRemainingNodes() : protocols::toolbox
• 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_past_virtual_residues() : protocols::denovo_design::components
• advance_to_neighbor_bin() : protocols::match
• aiModels_from_sfrs() : core::io::mmtf
• aiPose_from_sfr() : core::io::mmtf
• alapose() : protocols::kinmatch
• align_mainchain_atoms() : protocols::helical_bundle
• align_mainchain_atoms_of_residue_range() : protocols::helical_bundle
• align_motif_pose() : core::scoring::motif
• align_motif_pose_break() : core::scoring::motif
• align_motif_pose_by_one_frame() : core::scoring::motif
• align_motif_pose_NCAC_super() : core::scoring::motif
• align_motif_pose_super() : core::scoring::motif
• align_naive() : core::sequence
• align_pose_and_add_rmsd_constraints() : protocols::stepwise::modeler::align
• align_poses() : protocols::stepwise::modeler::rna
• align_poses_naive() : core::sequence
• align_to_native() : protocols::antibody
• align_virtual_atoms_in_carbohydrate_residue() : core::conformation::carbohydrates , core::pose::carbohydrates
• alignaxis() : protocols::matdes , protocols::sic_dock
• alignaxis_xform() : protocols::sic_dock
• alignment_from_pose() : core::sequence
• alignment_into_pose() : core::sequence
• alignment_probabilities() : protocols::medal
• alignments_from_cmd_line() : protocols::comparative_modeling
• AlignPDBInfoToSequences_namer() : protocols::pdbinfo_manipulations
• alignpdbinfotosequencesmode_to_string() : protocols::pdbinfo_manipulations
• all_atom_center() : core::conformation , core::pose
• all_atom_rmsd() : core::scoring
• all_atom_rmsd_nosuper() : core::scoring
• all_false_selection() : core::select::residue_selector
• all_pose_residues() : protocols::rna::movers
• all_scatom_rmsd_nosuper() : core::scoring
• all_true_selection() : core::select::residue_selector
• allifnone() : protocols::kinmatch
• allocate_matrix() : protocols::frag_picker::scores
• alpha_deriv_func() : core::scoring::fiber_diffraction
• alpha_func() : core::scoring::fiber_diffraction
• ambiguous_constraint_wrap() : protocols::constraint_generator
• analyze_base_bin_map() : protocols::stepwise::modeler::rna::rigid_body
• analyze_for_homology() : core::fragment::rna
• ANCHOR_TARGET() : protocols::anchored_design
• AND_combine() : core::select::residue_selector
• ang_delta() : protocols::environment , protocols::loops::loop_mover
• angle_between() : protocols::rigid
• angle_cpy() : protocols::abinitio::abscript
• angle_diff() : protocols::abinitio::abscript
• angle_distance() : core::scoring::motif
• angles() : core::scoring , core::scoring::packstat::old , core::scoring::sasa
• annotate_backbone() : core::chemical
• annotated_atom_graph_from_conformation() : core::conformation
• annotated_to_oneletter_sequence() : core::pose
• antibody_grafting_usable() : protocols::antibody::grafting
• any_atoms_within_cutoff() : core::select::util
• append_fold_tree_to_file() : protocols::backrub
• append_mg_bound_water() : protocols::magnesium
• append_new_chain_from_template_segment() : protocols::denovo_design::components
• append_new_residues() : protocols::denovo_design::components
• append_pose_by_bond() : protocols::indexed_structure_store
• append_pose_to_pose() : core::pose
• append_pose_to_pose_keep_fold_tree() : protocols::fold_from_loops::utils
• append_pose_with_glycan_residues() : core::pose
• append_pose_with_overlap() : protocols::indexed_structure_store
• append_residue_selector_subelements() : protocols::jd3
• append_residues_from_template_segment() : protocols::denovo_design::components
• append_rsd_by_jump_near_atom() : protocols::pose_metric_calculators
• append_single_far_away_water() : protocols::hydrate
• append_single_scorefxn_subelement() : protocols::jd3
• append_subelement_and_attributes_for_parse_loops_from_tag() : protocols::loop_modeling::utilities
• append_subelement_for_parse_movemap_factory_legacy() : protocols::rosetta_scripts
• append_subpose_to_pose() : core::pose
• append_virtual_residue_to_full_model_info() : core::pose::full_model_info
• apply_adducts_to_residue() : core::chemical
• apply_Aform_torsions() : core::pose::rna
• apply_best_scoring_fragdata() : core::fragment
• apply_chi_cst() : protocols::stepwise::legacy::modeler::rna
• apply_dofs() : core::pose::copydofs
• apply_full_to_sub_mapping() : protocols::stepwise::modeler::rna
• apply_ideal_c2endo_sugar_coords() : core::pose::rna
• apply_ideal_coordinates_for_alternative_pucker() : protocols::simple_moves
• apply_non_main_chain_sugar_coords() : core::pose::rna
• apply_numbering() : protocols::stepwise::modeler
• apply_protonated_H1_adenosine_variant_type() : protocols::stepwise::modeler::rna
• apply_pucker() : core::pose::rna
• apply_residue_entries_to_pose() : protocols::indexed_structure_store
• apply_rotamer() : protocols::stepwise::legacy::modeler::rna
• apply_rotate() : protocols::ligand_docking
• apply_sequence_mapping() : protocols::loops
• apply_set_weights() : core::scoring
• apply_sub_to_full_mapping() : protocols::stepwise::modeler::rna
• apply_suite_torsion_info() : core::pose::rna
• apply_superposition_transform() : protocols::toolbox
• apply_superposition_transform_to_jump() : protocols::toolbox
• apply_symm_gly_corrections() : core::chemical
• apply_tensor_transformation() : core::scoring::nmr
• apply_transformation() : protocols::forge::methods , protocols::hybridization
• apply_vector_rotation() : core::scoring::nmr
• apply_vector_transformation() : core::scoring::nmr
• apply_virtual_rna_residue_variant_type() : core::pose::rna
• archive_size_for_pose() : protocols::multistage_rosetta_scripts
• are_selections_equal() : core::select::residue_selector
• are_seqs_different() : protocols::vip
• arg_max() : protocols::mean_field
• arg_min() : protocols::mean_field
• argrot_dna_dis2() : protocols::dna
• as_set() : protocols::medal
• assemble_remark_line() : protocols::toolbox::match_enzdes_util
• assert_phosphate_nomenclature_matches_mini() : core::pose::rna
• assign_abase_derivs() : core::scoring::hbonds
• assign_gasteiger_atom_types() : core::chemical::gasteiger
• assign_initial_medoids() : protocols::multistage_rosetta_scripts::cluster
• assign_initial_medoids_on_the_fly() : protocols::multistage_rosetta_scripts::cluster
• assign_medoids() : protocols::multistage_rosetta_scripts::cluster
• assign_medoids_on_the_fly() : protocols::multistage_rosetta_scripts::cluster
• assign_non_medoids_to_clusters() : protocols::multistage_rosetta_scripts::cluster
• assign_non_medoids_to_clusters_on_the_fly() : protocols::multistage_rosetta_scripts::cluster
• assign_pucker() : core::pose::rna
• assign_random_continuous_rotamer() : core::pack
• assign_random_rotamers() : core::pack
• assign_rna_atom_type() : core::scoring::elec
• assign_ss_dssp() : protocols::jumping
• at_interface() : protocols::constel
• atom_dist_with_zero() : protocols::splice
• atom_distance() : protocols::protein_interface_design::filters , protocols::simple_filters
• atom_graph_from_conformation() : core::conformation
• atom_id_to_named_atom_id() : core::conformation , core::pose
• atom_is_acceptor() : core::pose::rna
• atom_is_aro() : core::scoring::elec
• atom_is_aro2() : core::scoring::elec
• atom_is_hydratable() : protocols::hydrate
• atom_is_polar() : core::pose::rna
• atom_map_valid_size() : protocols::hybridization
• atom_specific_rms() : protocols::motifs
• atom_square_deviation() : protocols::stepwise::modeler::rna
• atom_tracer() : protocols::ligand_docking
• atom_tree_dfunc() : core::optimization , core::optimization::symmetry
• atom_tree_get_atompairE_deriv() : core::optimization , core::optimization::symmetry
• atomic_depth() : core::scoring::atomic_depth
• atoms_deeper_than() : core::scoring::atomic_depth
• atoms_have_bond_to_bonded_atoms() : protocols::rna::movers
• atoms_have_mutual_bond_to_atom() : protocols::rna::movers
• atoms_interact() : core::scoring::methods
• attach_debugger() : protocols::optimize_weights
• attach_n_and_c_unfolded_poses_to_pose() : protocols::fold_from_loops::utils
• attach_unfolded_pose_to_pose_c_term() : protocols::fold_from_loops::utils
• attach_unfolded_pose_to_pose_n_term() : protocols::fold_from_loops::utils
• attachment_type_from_string() : protocols::stepwise::monte_carlo::mover
• attributes_for_get_ab_design_global_scorefxn() : protocols::antibody::design
• attributes_for_get_ab_design_min_scorefxn() : protocols::antibody::design
• attributes_for_get_cdr_bool_from_tag() : protocols::antibody
• attributes_for_get_resnum_selector() : core::pose
• attributes_for_get_resnum_string() : core::pose
• attributes_for_get_score_function_name() : core::scoring
• attributes_for_get_score_function_name_w_description() : core::scoring
• attributes_for_load_loop_definitions() : protocols::loops::loops_definers
• attributes_for_parse_constraint_generators() : protocols::constraint_generator
• attributes_for_parse_database_session() : protocols::rosetta_scripts
• attributes_for_parse_grid_set_from_tag() : protocols::qsar::scoring_grid
• attributes_for_parse_jump_selector() : core::select::jump_selector
• attributes_for_parse_jump_selector_default_option_name() : core::select::jump_selector
• attributes_for_parse_jump_selector_when_required() : core::select::jump_selector
• attributes_for_parse_movemap_factory() : core::select::movemap
• attributes_for_parse_movemap_factory_default_attr_name() : core::select::movemap
• attributes_for_parse_movemap_factory_when_required() : core::select::movemap
• attributes_for_parse_movemap_factory_when_required_default_name() : core::select::movemap
• attributes_for_parse_optional_grid_set_from_tag() : protocols::qsar::scoring_grid
• attributes_for_parse_residue_level_operations() : core::pack::task::operation
• attributes_for_parse_residue_selector() : core::select::residue_selector , protocols::rosetta_scripts
• attributes_for_parse_residue_selector_default_option_name() : core::select::residue_selector
• attributes_for_parse_residue_selector_logic_string() : core::select::residue_selector
• attributes_for_parse_residue_selector_when_required() : core::select::residue_selector
• attributes_for_parse_resnum() : core::pose
• attributes_for_parse_score_function() : core::scoring
• attributes_for_parse_score_function_w_description() : core::scoring
• attributes_for_parse_score_function_w_description_when_required() : core::scoring
• attributes_for_parse_task_operations() : core::pack::task
• attributes_for_parse_task_operations_w_factory() : core::pack::task
• attributes_for_parse_xyz_vector() : protocols::rosetta_scripts
• attributes_for_saved_reference_pose() : core::pose , protocols::rosetta_scripts
• attributes_for_saved_reference_pose_w_description() : core::pose , protocols::rosetta_scripts
• attributes_for_set_scorefxn_from_tag() : protocols::loop_modeling::utilities
• attributes_for_set_task_factory_from_tag() : protocols::loop_modeling::utilities
• auto_detect_atoms() : core::scoring::constraints
• auto_setup_all_metal_bonds() : core::util
• auto_setup_all_metal_constraints() : core::util
• auto_trim_floppy_termini() : protocols::sic_dock
• auto_use_linmem_ig() : core::pack::interaction_graph
• automorphic_rmsd() : core::scoring
• average_antiparallel_embeddings() : protocols::membrane
• average_embeddings() : protocols::membrane
• avg_ca_position() : protocols::nonlocal