- c -

• CA_gdtmm() : core::scoring
• CA_gdttm() : core::scoring
• CA_maxsub() : core::scoring
• CA_maxsub_by_subset() : core::scoring
• CA_rmsd() : core::scoring
• CA_rmsd_symmetric() : core::scoring
• calc_atom_masks() : core::scoring
• calc_interacting_vector() : core::pack::task::operation::util
• calc_interface_vector() : core::pack::task::operation::util
• calc_per_atom_sasa() : core::scoring
• calc_per_atom_sasa_sc() : core::scoring
• calc_per_res_hydrophobic_sasa() : core::scoring
• calc_total_sasa() : core::scoring
• calculate_intra_res_hbonds() : core::scoring::hbonds
• calculate_rigid_matrix() : core::chemical
• calpha_superimpose_pose() : core::scoring
• calpha_superimpose_with_mapping() : core::sequence
• canonical_atom_count() : core::pose
• canonical_residue_count() : core::pose
• 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
• cavity_distance_constraint() : core::scoring::packstat
• cbeta_vector() : core::pack::task::operation::util
• center_of_mass() : core::pose
• CENTROID() : core::chemical
• centroid_pose_from_pdb() : core::import_pose
• CENTROID_ROT() : core::chemical
• CENTROID_WTS() : core::scoring
• chain_gws_string() : core::io::carbohydrates
• change_cys_state() : core::conformation
• char_valid_as_torsion_bin() : core::conformation
• check_all_residues_sampled() : core::pose::full_model_info
• check_and_correct_sister_atom_based_on_chirality() : core::io::pdb
• check_and_correct_sister_atom_based_on_outgroup() : core::io::pdb
• check_and_correct_sister_atoms() : core::io::pdb
• check_binary_chars() : core::io::serialization
• check_binary_unsigned_int() : core::io::serialization
• check_deprecated_flags() : core::init
• check_full_model_info_OK() : core::pose::full_model_info
• check_good_neighbor() : core::conformation
• check_score_function_sanity() : core::init
• check_surface_area_leerichards_deriv() : core::scoring::packstat
• chi1_torsion_atom() : core::chemical::rna
• chi1_torsion_atom_index() : core::chemical::rna
• chi2_torsion_atom_index() : core::scoring::hackaro
• chi_continuation() : core::conformation
• chi_interruption() : core::conformation
• choose_effective_sequence_separation() : core::scoring::constraints
• chop_fragments() : core::fragment
• chr_chains() : core::chemical , core::conformation::symmetry
• cis_omega_torsion_bin() : core::conformation
• classify_base_pairs() : core::pose::rna
• clearPoseExtraScore() : core::pose
• clearPoseExtraScores() : core::pose
• clone() : core::io::serialization
• cmp_particles() : core::optimization
• COARSE_RNA() : core::chemical
• COARSE_TWO_BEAD() : core::chemical
• combinable() : core::scoring::constraints
• combine_constraints() : core::scoring::constraints
• combine_NMR_atom_string() : core::scoring::constraints
• combine_sequence_mappings() : core::id
• comma_strings_to_map() : core::conformation::symmetry
• comma_strings_to_pair_map() : core::conformation::symmetry
• comma_strings_to_vector() : core::conformation::symmetry
• comma_strings_to_vector_map() : core::conformation::symmetry
• comment_begin() : core::pack::task
• compact_enum_set() : core::chemical::gasteiger
• 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_simple_inteaction_graph_alt_state_and_energy_graph() : core::pack
• compute_and_store_pose_waters() : core::scoring::methods
• compute_atom_packing_scores() : core::scoring::packstat
• 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_coefficients3() : core::scoring::electron_density::SplineInterp
• compute_coefficients4() : 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_residue_packing_score() : core::scoring::packstat
• compute_residue_packing_scores() : core::scoring::packstat
• compute_rosettaholes_score() : core::scoring::packing
• compute_sasa() : core::scoring::packstat
• compute_sasa_generic() : core::scoring::packstat
• compute_sc_centroid() : core::scoring
• compute_sc_radius() : core::scoring
• compute_smooth_nb_deriv() : core::scoring::packing
• compute_surface_area_leerichards() : core::scoring::packstat
• compute_surface_area_leerichards_deriv() : core::scoring::packstat
• compute_surrounding_sasa() : core::scoring::packstat
• conf2pdb_chain() : core::pose
• conf2pdb_chain_default_map() : core::pose
• conj_map_times() : core::scoring::electron_density
• connection_indices() : core::scoring::mm
• const_full_model_info() : core::pose::full_model_info
• Contain_seq_num() : core::scoring::rna::chemical_shift
• convert_acgu_to_1234() : core::chemical::rna
• convert_atom_name() : core::io::pdb
• convert_from_std_map() : core::pose
• convert_inorder_table_to_original_order() : core::scoring::trie
• convert_inorder_vector_to_original_order() : core::scoring::trie
• convert_nucleic_acid_atom_name_to_standard() : core::io::pdb
• convert_nucleic_acid_atom_names_to_standard() : core::io::pdb
• convert_nucleic_acid_residue_info_to_standard() : core::io::pdb
• convert_res_name() : core::io::pdb
• convert_residuetype_to_light_graph() : core::chemical
• convert_to_BondName() : core::chemical
• convert_to_ResidueType() : core::chemical::sdf
• ConvertToInterpolationCoefficients() : core::scoring::electron_density::SplineInterp
• convolute_maps() : core::scoring::electron_density
• copy_dofs() : core::pose::copydofs
• copy_dofs_match_atom_names() : core::pose::copydofs
• copy_residue_coordinates_and_rebuild_missing_atoms() : core::conformation
• correctly_add_cutpoint_variants() : core::pose , core::pose::rna
• correctly_position_cutpoint_phosphate_torsions() : core::pose::rna
• count_atom() : core::scoring::methods
• count_constraint() : core::scoring::constraints
• count_pair_bs() : core::scoring::methods
• create_acc_orientation_vector() : core::scoring::hbonds
• create_bond_length() : core::chemical
• 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_minimization_graph() : core::pack
• create_oriented_water_rotamer() : core::pack::rotamer_set
• create_packer_graph() : core::pack
• create_rotamer_descriptor() : core::scoring::hbonds
• create_sasa_method() : core::scoring::sasa
• create_scmin_minimizer_map() : core::pack
• create_shuffle_map_recursive_rms() : core::scoring
• create_subpose() : core::pose
• create_trie() : core::scoring::trie
• cst_eq() : core::scoring::constraints
• cull_violators() : core::scoring::constraints