- c -

• C_METHYLAMIDATION() : core::chemical
• CA_gdtmm() : core::scoring
• CA_maxsub() : core::scoring
• CA_maxsub_by_subset() : core::scoring
• CA_rmsd() : core::scoring
• CA_rmsd_symmetric() : core::scoring
• CA_superimpose() : protocols::toolbox
• calc_all_averages() : protocols::unfolded_state_energy_calculator
• calc_all_dist() : protocols::MakeRotLib
• calc_atom_masks() : core::scoring
• calc_centroids() : protocols::MakeRotLib
• calc_delta_sasa() : protocols::fldsgn::topology
• calc_dist() : protocols::MakeRotLib
• calc_fit_R() : protocols::toolbox
• calc_Fnat() : protocols::docking
• calc_interacting_vector() : core::pack::task::operation::util
• calc_interaction_energy() : protocols::docking
• calc_interface_vector() : core::pack::task::operation::util
• calc_Irmsd() : protocols::docking
• calc_Lrmsd() : protocols::docking
• calc_pareto_front() : protocols::design_opt
• calc_per_atom_sasa() : core::scoring
• calc_per_res_hydrophobic_sasa() : core::scoring
• calc_per_residue_scores() : protocols::sparta
• calc_res_contact() : protocols::docking
• calc_rotamer_clusters() : protocols::MakeRotLib
• calc_std_dev() : protocols::MakeRotLib
• calc_strand_pairing_set() : protocols::fldsgn::topology
• calc_total_sasa() : core::scoring
• calc_vector_boltzmann() : protocols::unfolded_state_energy_calculator
• calc_vector_mean() : protocols::unfolded_state_energy_calculator
• calc_vector_median() : protocols::unfolded_state_energy_calculator
• calc_vector_mode() : protocols::unfolded_state_energy_calculator
• calculate_carbohydrate_phi() : core::pose::carbohydrates
• calculate_ccd_angle() : protocols::loops::loop_closure::ccd
• calpha_superimpose_pose() : core::scoring
• calpha_superimpose_with_mapping() : core::sequence
• canonical_atom_count() : core::pose
• canonical_residue_count() : core::pose
• canonical_sampling_main() : protocols::canonical_sampling
• carbohydrate_phi_offset_from_BB() : core::pose::carbohydrates
• CARBOXYLATION() : core::chemical
• cart_numerical_derivative_check() : core::optimization
• cartesian_collect_atompairE_deriv() : core::optimization
• cartesian_collect_torsional_deriv() : core::optimization
• cartesian_dfunc() : core::optimization
• case_from_lines() : core::chemical
• catalytic_res() : protocols::enzdes::enzutil
• cavity_distance_constraint() : core::scoring::packstat
• cb_weight() : protocols::sic_dock
• cb_weight_map_from_pose() : protocols::sic_dock
• cb_weights_from_pose() : protocols::sic_dock
• cbeta_vector() : core::pack::task::operation::util
• ccd_close_loops() : protocols::loops
• ccd_moves() : protocols::loops::loop_closure::ccd
• CDR_H3_cter_filter() : protocols::antibody2
• CDR_H3_filter_legacy_code_with_old_rule() : protocols::antibody2
• center_of_mass() : protocols::geometry
• CENTROID() : core::chemical
• CENTROID_HA() : core::chemical
• centroid_pair_by_jump() : protocols::geometry
• centroid_pose_from_pdb() : core::import_pose
• CENTROID_WTS() : core::scoring
• centroids_by_jump() : protocols::geometry
• centroids_by_jump_int() : protocols::geometry
• CHAINBREAK_WEIGHT() : protocols::anchored_design
• change_cys_state() : core::conformation
• check_all_ligand_atoms() : protocols::ligand_docking::ligand_options
• check_base_pair() : protocols::rna
• check_binary_chars() : core::io::serialization
• check_binary_unsigned_int() : core::io::serialization
• Check_chain_closable() : protocols::swa::rna
• Check_chain_closable_floating_base() : protocols::swa::rna
• check_deprecated_flags() : core
• check_domain_map() : core::pose
• check_floating_base_chain_closable() : protocols::swa::rna
• check_for_messed_up_structure() : protocols::swa::rna
• check_good_neighbor() : core::conformation
• check_in_base_pair_list() : protocols::rna
• check_internal_hbonds() : protocols::fldsgn::topology
• check_is_working_res() : protocols::swa::rna
• check_kink_helix() : protocols::fldsgn::topology
• check_neighbor_ligand_atom() : protocols::ligand_docking::ligand_options
• check_overlap_pos() : protocols::loops::loop_closure::ccd
• check_required() : protocols::star
• check_required_cm() : protocols::medal
• check_required_common() : protocols::medal
• check_RMSD() : protocols::ligand_docking
• check_score() : protocols::ligand_docking
• check_scorefxn_has_constraint_terms_if_pose_has_constraints() : protocols::swa
• check_surface_area_leerichards_deriv() : core::scoring::packstat
• check_torsions() : protocols::loops::loop_closure::ccd
• check_validity_and_get_working_res() : protocols::swa::rna
• checkpoint_cleanup() : protocols::dna
• checkpoint_with_interval() : protocols::checkpoint
• chi1_torsion_atom() : core::scoring::rna
• chi1_torsion_atom_index() : core::scoring::rna
• chi2_torsion_atom_index() : core::scoring::hackaro
• chi_continuation() : core::conformation
• chi_interruption() : core::conformation
• chis_from_pose() : protocols::comparative_modeling
• choose_effective_sequence_separation() : core::scoring::constraints
• chop_fragments() : core::fragment
• chr_chains() : core::io::pdb , core::pose
• chunk_probabilities() : protocols::medal
• chunks_by_CA_CA_distance() : protocols::nonlocal
• classify_base_pairs() : protocols::rna
• clear_conformation_viewers() : protocols::viewer
• clearPoseExtraScore() : core::pose
• clearPoseExtraScores() : core::pose
• clone() : core::io::serialization
• close_chainbreaks() : protocols::jumping
• close_to_dna() : protocols::dna
• closed_range() : protocols::forge::methods
• closest_larger_peptide_vertex() : protocols::forge::methods
• closest_smaller_peptide_vertex() : protocols::forge::methods
• cluster_silent_structs() : protocols::toolbox
• cm_main() : protocols::comparative_modeling
• cmp() : protocols::loophash
• cmp_pair_by_first_vec_val() : protocols::design_opt
• cmp_pair_by_second() : protocols::design_opt
• cmp_pair_vec_by_first_vec_val() : protocols::design_opt
• cmp_particles() : core::optimization
• COARSE_RNA() : core::chemical
• COARSE_TWO_BEAD() : core::chemical
• combinable() : core::scoring::constraints
• combine_and_trim() : protocols::nonlocal
• combine_constraints() : core::scoring::constraints
• combine_loops() : protocols::medal
• combine_NMR_atom_string() : core::scoring::constraints
• combine_sequence_mappings() : core::id
• combine_two_poses() : protocols::seeded_abinitio
• comma_strings_to_map() : core::conformation::symmetry
• comma_strings_to_vector() : core::conformation::symmetry
• comma_strings_to_vector_map() : core::conformation::symmetry
• comment_begin() : core::pack::task
• common_setup() : protocols::abinitio
• compare() : protocols::fldsgn::topology
• compare_atom_coordinates() : core::pose
• compare_binary_protein_silent_struct() : core::pose
• compare_by_abs() : core::scoring
• compare_mingraph_and_energy_graph() : core::pack
• compare_RNA_char() : protocols::rna
• compare_RNA_secstruct() : protocols::rna
• compare_simple_inteaction_graph_alt_state_and_energy_graph() : core::pack
• compareIndexEnergyPair() : protocols::cluster , protocols::toolbox
• compareRef_fxn() : protocols::sparta
• complete_connections_tracer() : protocols::ligand_docking
• compute_and_store_pose_waters() : core::scoring::methods
• compute_atom_packing_scores() : core::scoring::packstat
• compute_avge_scores() : protocols::sasa_scores
• compute_bb_centroid() : core::scoring
• compute_bb_radius() : core::scoring
• compute_cav_ball_clusters() : core::scoring::packstat
• compute_cav_ball_neighbor_count() : core::scoring::packstat
• compute_cav_ball_volumes() : core::scoring::packstat
• compute_coefficients() : core::scoring::electron_density::SplineInterp
• compute_dec15_score() : core::scoring::packing
• compute_exact_geosol() : core::scoring::geometric_solvation
• compute_holes_deriv() : core::scoring::packing
• compute_holes_deriv_res() : core::scoring::packing
• compute_holes_score() : core::scoring::packing
• compute_holes_score_res() : core::scoring::packing
• compute_holes_surfs() : core::scoring::packing
• compute_jump_rmsd() : core::scoring
• compute_packing_score() : core::scoring::packstat
• compute_packing_score_leerichards() : core::scoring::packstat
• compute_per_residue_coverage() : core::fragment
• compute_per_residue_probabilities() : protocols::star
• compute_residue_packing_score() : core::scoring::packstat
• compute_residue_packing_scores() : core::scoring::packstat
• compute_residue_sasas_for_sasa_scores() : protocols::sasa_scores
• compute_rosettaholes_score() : core::scoring::packing
• compute_sasa() : core::scoring::packstat
• compute_sasa_generic() : core::scoring::packstat
• compute_sasapack_scores() : protocols::sasa_scores
• compute_sc_centroid() : core::scoring
• compute_sc_radius() : core::scoring
• compute_smooth_nb_deriv() : core::scoring::packing
• compute_ss_regions() : protocols::loops
• compute_surface_area_leerichards() : core::scoring::packstat
• compute_surface_area_leerichards_deriv() : core::scoring::packstat
• compute_surrounding_sasa() : core::scoring::packstat
• concatenate_profiles() : protocols::protein_interface_design::movers
• conf2pdb_chain() : core::pose
• configure_rmc() : protocols::star
• connect_from() : protocols::protein_interface_design::movers
• connect_to() : protocols::protein_interface_design::movers
• connected_mainchain_atomids() : protocols::backrub
• connection_indices() : core::scoring::mm
• connects_rigid_regions() : protocols::topology_broker
• const_sub_to_full_info_from_pose() : protocols::swa::monte_carlo
• constrain_ligand_torsions() : protocols::ligand_docking
• constrain_pose_res_to_invrots() : protocols::toolbox::match_enzdes_util
• constraint_set_slice() : protocols::swa
• constraints_NtoC() : protocols::flxbb
• constraints_sheet() : protocols::flxbb
• construct_poly_ala_pose() : protocols::toolbox::pose_manipulation
• construct_poly_uniq_restype_pose() : protocols::toolbox::pose_manipulation
• construct_poly_XXX_pose() : protocols::toolbox::pose_manipulation
• contact_distance2() : protocols::dna
• contact_name() : protocols::frag_picker
• contact_type() : protocols::frag_picker
• Contain_residue_at_seq_num() : protocols::swa::rna
• Contain_seq_num() : core::scoring::rna::chemical_shift , protocols::swa , protocols::swa::rna
• contains() : protocols::sparta
• contains_stageid() : protocols::abinitio
• convert_acgu_to_1234() : core::scoring::rna
• convert_atom_name() : core::io::pdb
• convert_based_on_match_type() : protocols::rna
• convert_cartesian_to_spherical_coor_triplet() : protocols::pockets
• convert_euler_to_coordinate_matrix() : protocols::swa::rna
• convert_inorder_table_to_original_order() : core::scoring::trie
• convert_inorder_vector_to_original_order() : core::scoring::trie
• Convert_rebuild_residue_string_to_list() : protocols::swa::rna
• convert_res_name() : core::io::pdb
• convert_spherical_coor_triplet_to_cartesian() : protocols::pockets
• convert_to_working_res() : protocols::swa
• ConvertToInterpolationCoefficients() : core::scoring::electron_density::SplineInterp
• coordinate_constrain_selection() : protocols::relax
• copy_all_o2star_torsions() : protocols::swa::rna
• copy_bulge_res_and_ribose_torsion() : protocols::swa::rna
• copy_dofs() : core::pose
• copy_dofs_match_atom_names() : core::pose
• copy_hotspot_to_pose() : protocols::protein_interface_design::movers
• copy_internal_coords() : protocols::topology_broker
• copy_residue_coordinates_and_rebuild_missing_atoms() : core::conformation
• copy_residues() : protocols::star
• copy_side_chains() : protocols::abinitio
• copy_stretch() : protocols::protein_interface_design::movers
• copy_torsions_FROM_TO() : protocols::swa::rna
• copy_torsions_to_pose() : protocols::loops::loop_closure::ccd
• Correctly_position_cutpoint_phosphate_torsions() : protocols::swa::rna
• count_atom() : core::scoring::methods
• count_buried_unsat_Hbonds() : protocols::ligand_docking
• count_CBs() : protocols::sic_dock
• count_constraint() : core::scoring::constraints
• count_cutpoints() : protocols::forge::methods
• count_linkers() : protocols::sic_dock
• count_pair_bs() : core::scoring::methods
• covalent_compliance() : protocols::noesy_assign
• create_acc_orientation_vector() : core::scoring::hbonds
• create_alignment_id_map() : protocols::swa , protocols::swa::rna , protocols::swa
• create_cache() : protocols::frag_picker::scores
• create_command_map() : core::pack::task
• create_cpdata_correspondence_for_rotamer() : core::scoring::trie
• create_cpdata_correspondence_for_rotamerset() : core::scoring::trie
• create_don_orientation_vector() : core::scoring::hbonds
• create_euler_rotation() : protocols::swa
• create_extra_output() : protocols::floppy_tail
• create_fragment_set() : protocols::hybridization
• create_full_to_input_res_map() : protocols::swa::rna
• create_match_position_modifier() : protocols::match
• create_minimization_graph() : core::pack
• create_oriented_water_rotamer() : core::pack::rotamer_set
• create_packer_graph() : core::pack
• create_remark_headers_from_cstcache() : protocols::enzdes::enzutil
• create_rna_vall_torsions() : protocols::rna
• create_rotamer_descriptor() : core::scoring::hbonds
• create_scmin_minimizer_map() : core::pack
• create_shuffle_map_recursive_rms() : core::scoring
• create_standard_o2star_pack_task() : protocols::swa::rna
• Create_strand_list() : protocols::swa::rna
• create_subpose() : core::pose
• create_trie() : core::scoring::trie
• CSDAtomTypeSetcontains_atom_type() : core::chemical
• cst_residue_in_pose() : protocols::toolbox::match_enzdes_util
• ctabParserTracer() : core::chemical::sdf
• cull_violators() : core::scoring::constraints
• current_batch() : protocols::jd2
• current_job() : protocols::nonlocal
• current_output_filename() : protocols::jd2
• current_output_name() : protocols::jd2
• current_replica() : protocols::jd2
• CUTPOINT_LOWER() : core::chemical
• cutpoint_probabilities() : protocols::medal
• cutpoint_separation() : protocols::antibody2
• CUTPOINT_UPPER() : core::chemical
• cutpoints_separation() : protocols::antibody2
• cyclize_pose() : protocols::forge::methods