- 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
• add_atom() : core::kinematics
• add_atom_type_set_parameters_from_command_line() : core::chemical
• add_comment() : core::pose
• 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_coordinate_constraints() : core::scoring::constraints
• add_covalent_linkage() : core::util
• add_covalent_linkage_helper() : core::util
• add_covalent_linkages_to_metal() : core::util
• add_dens_scores_from_cmdline_to_scorefxn() : core::scoring::electron_density
• 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_hbs_constraint() : core::pose::ncbb
• add_lower_terminus_type_to_conformation_residue() : core::conformation
• add_lower_terminus_type_to_pose_residue() : core::pose
• add_oop_constraint() : core::pose::ncbb
• add_rna_chi_rotamers() : core::pack::rotamer_set
• add_score_line_string() : core::pose
• 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_values_from_center() : core::chemical::rna
• add_variant_type_to_conformation_residue() : core::conformation
• add_variant_type_to_pose_residue() : core::pose
• add_variant_type_to_residue() : core::pose
• add_whitespaces() : core::scoring::rna::chemical_shift
• addVirtualResAsRoot() : core::pose
• 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_poses_naive() : core::sequence
• align_virtual_atoms_in_carbohydrate_residue() : core::pose::carbohydrates
• alignment_from_pose() : core::sequence
• alignment_into_pose() : core::sequence
• all_atom_rmsd() : core::scoring
• all_atom_rmsd_nosuper() : core::scoring
• all_scatom_rmsd_nosuper() : core::scoring
• all_visited() : core::graph
• alpha_deriv_func() : core::scoring::fiber_diffraction
• alpha_func() : core::scoring::fiber_diffraction
• alternate_tricubic_interpolation() : core::pack::dunbrack
• 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
• any_atoms_within_cutoff() : core::pack::task::operation::util
• append_pose_to_pose() : core::pose
• 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_dofs() : core::pose::copydofs
• apply_ideal_c2endo_sugar_coords() : core::pose::rna
• apply_non_main_chain_sugar_coords() : core::pose::rna
• apply_pucker() : core::pose::rna
• apply_virtual_rna_residue_variant_type() : core::pose::rna
• 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
• asymmetrize_scorefunction() : core::scoring::symmetry
• at() : core::io::serialization
• 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_next_to_connect_atom() : core::pose::carbohydrates
• atom_tree_dfunc() : core::optimization , core::optimization::symmetry
• atom_tree_get_atompairE_deriv() : core::optimization , core::optimization::symmetry
• atoms_interact() : core::scoring::methods
• auto_detect_atoms() : core::scoring::constraints
• auto_setup_all_metal_bonds() : core::util
• auto_setup_all_metal_constraints() : core::util
• auto_setup_metal_bonds() : core::util
• automorphic_rmsd() : core::scoring