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• abego_index() : protocols::frag_picker::quota
• 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_conformation_viewer() : protocols::viewer
• add_constraints_from_file() : protocols::dna
• add_coordinate_constraints() : protocols::protein_interface_design::movers , protocols::seeded_abinitio
• add_coordinate_constraints_to_pose() : protocols::loops , protocols::relax
• add_cutpoint_variants() : protocols::forge::methods , protocols::loops
• add_dist_constraints() : protocols::seeded_abinitio
• add_edges() : protocols::forge::methods
• add_fade_chain_break_constraint_across_gap() : protocols::stepwise::sampling::rna
• add_harmonic_chain_break_constraint() : protocols::stepwise::sampling::rna
• add_harmonic_cluster_constraint() : protocols::antibody
• add_harmonic_cluster_constraints() : protocols::antibody
• add_hbs_constraint() : protocols::simple_moves::hbs
• 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_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_relevant_restypes_to_subset() : protocols::toolbox::match_enzdes_util
• add_single_cutpoint_variant() : protocols::loops
• add_strand_pairs_cst() : protocols::hybridization
• add_vall_cheating_fragments() : protocols::frags
• add_vall_fragments() : protocols::frags
• add_vec() : protocols::toolbox
• add_vertex() : protocols::forge::methods
• add_virtual_O2Prime_hydrogen() : protocols::stepwise::sampling::rna
• add_virtual_residue_to_cterm() : protocols::relax
• AddPyMolObserver() : protocols::moves
• addScoresForLoopParts() : protocols::loops
• 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_motif_pose_break() : protocols::motif_hash
• align_motif_pose_super() : protocols::motif_hash
• align_poses() : protocols::stepwise::sampling::rna
• align_to_native() : protocols::antibody
• alignaxis() : protocols::sic_dock
• alignaxis_xform() : protocols::sic_dock
• alignment_from_cmd_line() : protocols::comparative_modeling
• alignment_probabilities() : protocols::medal
• alignments_from_cmd_line() : protocols::comparative_modeling
• allifnone() : protocols::kinmatch
• allocate_matrix() : protocols::frag_picker::scores
• analyze_base_bin_map() : protocols::stepwise::sampling::rna::rigid_body
• angle_between() : protocols::rigid
• angle_diff() : protocols::MakeRotLib
• 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_chi_cst() : protocols::stepwise::sampling::rna::legacy
• apply_full_to_sub_mapping() : protocols::stepwise::sampling::rna
• apply_ideal_coordinates_for_alternative_pucker() : protocols::simple_moves
• apply_numbering() : protocols::stepwise
• apply_protonated_H1_adenosine_variant_type() : protocols::stepwise::sampling::rna
• apply_rotamer() : protocols::stepwise::sampling::rna
• apply_rotate() : protocols::ligand_docking
• apply_sequence_mapping() : protocols::loops
• apply_sub_to_full_mapping() : protocols::stepwise::sampling::rna
• apply_superposition_transform() : protocols::toolbox
• apply_superposition_transform_to_jump() : protocols::toolbox
• apply_transformation() : protocols::forge::methods , protocols::hybridization
• apply_virtual_rna_residue_variant_type() : protocols::stepwise::sampling::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_phosphate_nomenclature_matches_mini() : protocols::farna
• assign_ss_dssp() : protocols::jumping
• atom_is_acceptor() : protocols::farna
• atom_is_polar() : protocols::farna
• atom_map_valid_size() : protocols::hybridization
• atom_specific_rms() : protocols::motifs
• atom_square_deviation() : protocols::stepwise::sampling::rna
• attach_debugger() : protocols::optimize_weights
• attachment_type_from_string() : protocols::stepwise::monte_carlo
• auto_trim_floppy_termini() : protocols::sic_dock
• avg_ca_position() : protocols::nonlocal
• avg_cluster_cen_dist() : protocols::MakeRotLib