- a -

• a() : core::pose::motif
• aa2idx() : core::scoring::saxs
• aa2name() : core::chemical
• aa2oneletter() : core::chemical
• aa_from_name() : core::chemical
• aa_from_oneletter_code() : core::chemical
• aa_trustworthiness() : core::scoring::motif
• abego_index() : protocols::frag_picker::quota
• abego_str() : protocols::denovo_design
• abego_vector() : protocols::denovo_design
• absfpart() : protocols::cryst
• absolute_vec() : protocols::features::strand_assembly
• add_a3b_hbs_constraint() : core::pose::ncbb
• add_another_virtual_res() : protocols::toolbox::sample_around
• add_atom() : core::kinematics
• add_atom_type_set_parameters_from_command_line() : core::chemical
• add_block_stack_variants() : protocols::stepwise::setup
• add_chain_from_pose() : protocols::denovo_design
• add_chainbreaks_according_to_jumps() : protocols::toolbox::pose_manipulation
• add_claims_from_file() : protocols::topology_broker
• add_claims_from_stream() : protocols::topology_broker
• 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_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_cutpoint_closed() : protocols::stepwise::setup
• add_cutpoint_variants() : protocols::forge::methods , protocols::loops
• add_cutpoint_variants_for_ccd() : protocols::grafting
• add_cutpoints() : protocols::denovo_design::components
• 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_fade_chain_break_constraint_across_gap() : protocols::stepwise::modeler::rna
• add_generic_hbs_constraint() : core::pose::ncbb
• add_harmonic_chain_break_constraint() : protocols::stepwise::modeler::rna
• add_harmonic_dihedral_cst_general() : protocols::antibody::constraints
• add_hbs_constraint() : core::pose::ncbb , 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_linker_segments() : protocols::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_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_movemap_from_loopres() : protocols::mpi_refinement
• add_movemaps_to_datamap() : protocols::rosetta_scripts
• add_non_protein_cst() : protocols::hybridization
• add_num_neighbors() : protocols::sewing
• add_oop_constraint() : core::pose::ncbb
• add_overlap_to_loops() : protocols::denovo_design::movers
• add_poseinfo_to_ss() : protocols::mpi_refinement
• add_relevant_restypes_to_subset() : protocols::toolbox::match_enzdes_util
• add_remark() : protocols::denovo_design
• add_residues_to_pose() : protocols::denovo_design
• add_rna_chi_rotamers() : core::pack::rotamer_set
• add_score_line_string() : core::pose
• add_segment() : protocols::denovo_design::components
• add_segments_for_chain() : protocols::denovo_design::components
• add_single_cutpoint_variant() : protocols::loops
• add_single_magnesium() : protocols::magnesium
• add_strand_pairs_cst() : protocols::hybridization
• add_terminus_variants() : protocols::denovo_design::components
• add_to_individual_sol_energies() : core::scoring::geometric_solvation
• add_to_list() : protocols::denovo_design
• add_to_pose() : protocols::denovo_design::components
• add_to_pose_list() : protocols::stepwise::modeler
• 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_residues() : protocols::denovo_design::components
• add_virtual_sugar_res() : protocols::stepwise::setup
• add_whitespaces() : core::scoring::rna::chemical_shift
• AddPyMolObserver() : protocols::moves
• AddPyMolObserver_to_conformation() : protocols::moves
• AddPyMolObserver_to_energies() : protocols::moves
• addScoresForLoopParts() : protocols::loops
• 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_to_neighbor_bin() : protocols::match
• 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::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
• all_atom_rmsd() : core::scoring
• all_atom_rmsd_nosuper() : core::scoring
• all_scatom_rmsd_nosuper() : core::scoring
• all_visited() : core::graph
• 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
• ANCHOR_TARGET() : protocols::anchored_design
• ang_delta() : protocols::environment , protocols::loops::loop_mover
• angle_between() : protocols::rigid
• angle_cpy() : protocols::abinitio::abscript
• angle_diff() : protocols::abinitio::abscript , protocols::make_rot_lib
• angle_distance() : core::scoring::motif
• angles() : core::scoring , core::scoring::packstat::old , core::scoring::sasa
• 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_automorphic_rmsd() : protocols::ligand_docking
• append_fold_tree_to_file() : protocols::backrub
• 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_mg_bound_water() : protocols::magnesium
• append_multi_residue_ligand_RMSD() : protocols::ligand_docking
• append_new_chain_from_template_segment() : protocols::denovo_design::components
• append_new_residues() : protocols::denovo_design::components
• append_pose_to_pose() : core::pose
• append_pose_with_glycan_residues() : core::pose
• append_radius_of_gyration() : protocols::ligand_docking
• append_residues_from_template_segment() : protocols::denovo_design::components
• append_rsd_by_jump_near_atom() : protocols::toolbox::pose_metric_calculators
• append_subelement_for_parse_movemap() : protocols::rosetta_scripts
• append_subelement_for_parse_movemap_w_datamap() : protocols::rosetta_scripts
• append_subpose_to_pose() : core::pose
• 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_rotamer() : protocols::stepwise::legacy::modeler::rna
• apply_rotate() : protocols::ligand_docking
• apply_sequence_mapping() : protocols::loops
• 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_transformation() : protocols::forge::methods , protocols::hybridization
• apply_virtual_rna_residue_variant_type() : core::pose::rna
• are_seqs_different() : protocols::vip
• argrot_dna_dis2() : protocols::dna
• as_set() : protocols::medal
• asp_corrections() : protocols::make_rot_lib
• assemble_remark_line() : protocols::toolbox::match_enzdes_util
• assert_phosphate_nomenclature_matches_mini() : protocols::farna
• assign_abase_derivs() : core::scoring::hbonds
• assign_gasteiger_atom_types() : core::chemical::gasteiger
• 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
• asymmetrize_scorefunction() : core::scoring::symmetry
• atom_distance() : protocols::protein_interface_design::filters , protocols::simple_filters
• atom_graph_from_conformation() : core::conformation
• atom_id_from_icoor_line() : core::chemical
• 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_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
• atoms_interact() : core::scoring::methods
• attach_debugger() : protocols::optimize_weights
• attachment_type_from_string() : protocols::stepwise::monte_carlo::mover
• attributes_for_get_task_operations() : protocols::rosetta_scripts
• attributes_for_parse_score_function() : protocols::rosetta_scripts
• attributes_for_parse_task_operations() : protocols::rosetta_scripts
• attributes_for_parse_task_operations_w_factory() : protocols::rosetta_scripts
• 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
• automorphic_rmsd() : core::scoring
• average_antiparallel_embeddings() : protocols::membrane
• average_embeddings() : protocols::membrane
• avg_ca_position() : protocols::nonlocal
• avg_cluster_cen_dist() : protocols::make_rot_lib
• avoid_negative_zero() : protocols::analysis