- c -

• C() : protocols::sic_dock::scores
• C21() : protocols::sic_dock::scores
• C22() : protocols::sic_dock::scores
• C23() : protocols::sic_dock::scores
• C24() : protocols::sic_dock::scores
• C25() : protocols::sic_dock::scores
• C28() : protocols::sic_dock::scores
• C29() : protocols::sic_dock::scores
• C30() : protocols::sic_dock::scores
• c_array_mult() : core::scoring::fiber_diffraction
• c_mult_ip() : core::scoring::fiber_diffraction
• CA() : protocols::sic_dock::scores
• Ca_coord() : protocols::fold_from_loops::movers , protocols::simple_moves
• Ca_coords() : protocols::protein_interface_design::filters , protocols::simple_moves , protocols::splice
• CA_gdtmm() : core::scoring
• CA_gdttm() : core::scoring
• CA_maxsub() : core::scoring
• CA_maxsub_by_subset() : core::scoring
• CA_or_equiv_rmsd() : core::scoring
• CA_rmsd() : core::scoring
• CA_rmsd_symmetric() : core::scoring
• CA_Sscore() : protocols::mpi_refinement
• CA_superimpose() : protocols::toolbox
• cal_dis_angle_to_find_sheet() : protocols::features::strand_assembly
• cal_min_avg_dis_between_sheets_by_cen_res() : protocols::features::strand_assembly
• cal_min_avg_dis_between_two_sheets_by_cen_res() : protocols::features::strand_assembly
• cal_min_dis_between_sheets_by_all_res() : protocols::features::strand_assembly
• cal_min_dis_between_two_sheets_by_all_res() : protocols::features::strand_assembly
• cal_num_of_sheets_that_surround_this_sheet() : protocols::features::strand_assembly
• cal_shortest_dis_between_facing_aro_in_sw() : protocols::features::strand_assembly
• calc_all_averages() : protocols::unfolded_state_energy_calculator
• calc_angle_rmsd() : protocols::membrane
• calc_approx_loop_length() : protocols::denovo_design::connection
• calc_atom_masks() : core::scoring
• calc_base_centroid_rmsd() : protocols::recces::sampler::rna
• calc_CA_Irmsd() : protocols::docking
• calc_CAPRI_rank() : protocols::docking
• calc_delta_sasa() : protocols::fldsgn::topology
• calc_dihedral() : protocols::denovo_design::movers
• calc_fit_R() : protocols::toolbox
• calc_Fnat() : protocols::docking
• calc_Fnonnat() : protocols::docking
• calc_helix_axis() : protocols::membrane
• calc_helix_tilt_angle() : protocols::membrane
• calc_interacting_vector() : core::select::util
• calc_interaction_energy() : protocols::docking
• calc_interface_vector() : core::select::util
• calc_intf_score() : protocols::docking
• calc_Irmsd() : protocols::docking
• calc_Irmsd_legacy() : protocols::docking
• calc_Lrmsd() : protocols::docking
• calc_mean() : protocols::monte_carlo
• calc_P1rmsd() : protocols::docking
• calc_P2rmsd() : protocols::docking
• calc_paired_residues() : protocols::denovo_design::components
• calc_pareto_front() : protocols::design_opt , protocols::matdes
• calc_pareto_front_nbrs() : protocols::design_opt , protocols::matdes
• calc_per_atom_sasa() : core::scoring
• calc_per_atom_sasa_sc() : core::scoring
• calc_per_res_hydrophobic_sasa() : core::scoring
• calc_per_residue_scores() : protocols::sparta
• calc_per_rsd_score() : core::scoring::electron_density
• calc_res_contact() : protocols::docking
• calc_rsd_sasa() : protocols::forge::methods
• calc_strand_helix_angle() : protocols::fldsgn::topology
• calc_strand_pairing_set() : protocols::fldsgn::topology
• calc_sum() : protocols::monte_carlo
• calc_sum_squares() : protocols::monte_carlo
• calc_sum_xy() : protocols::monte_carlo
• 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_chi2_free() : core::scoring::fiber_diffraction
• calculate_chi_k() : core::scoring::fiber_diffraction
• calculate_density_nbr() : core::scoring::electron_density
• calculate_derivatives_gpu() : core::scoring::fiber_diffraction
• calculate_dihedral_distance() : protocols::antibody::clusters
• calculate_dihedral_w_4_resnums() : protocols::features::strand_assembly
• calculate_geometry() : core::scoring::electron_density
• calculate_I_of_E() : core::scoring::fiber_diffraction
• calculate_intensity_gpu() : core::scoring::fiber_diffraction
• calculate_intra_res_hbonds() : core::scoring::hbonds
• calculate_inverting_virtuals() : core::conformation::symmetry
• calculate_point_in_cone() : core::select::util
• calculate_rama() : core::scoring::electron_density
• calculate_rigid_matrix() : core::chemical
• calculate_rmsd() : protocols::splice
• calculate_statistics() : protocols::ncbb
• calculate_water_overcoordinated_hb_correction() : protocols::hydrate
• calDist() : protocols::pockets
• calpha_superimpose_pose() : core::scoring
• calpha_superimpose_with_mapping() : core::sequence
• can_hydrogen_bond() : protocols::constraint_generator
• canonical_atom_count() : core::pose
• canonical_residue_count() : core::pose
• canonical_sampling_main() : protocols::canonical_sampling
• canonicalize() : protocols::denovo_design::components
• cart_numerical_derivative_check() : core::optimization
• cartesian_collect_atompairE_deriv() : core::optimization
• cartesian_collect_torsional_deriv() : core::optimization
• cartesian_dfunc() : core::optimization
• CartesianSampler_subelement_ct_name() : protocols::hybridization
• case_from_lines() : core::chemical
• catalytic_res() : protocols::enzdes::enzutil
• cavity_distance_constraint() : core::scoring::packstat
• CB() : protocols::sic_dock::scores
• cb_coord_() : core::scoring::epr_deer
• cb_weight() : protocols::sic_dock
• cb_weight_map_from_pose() : protocols::sic_dock
• cb_weights_from_map() : protocols::sic_dock
• cb_weights_from_pose() : protocols::sic_dock
• cbeta_vector() : core::select::util
• CBlocal() : protocols::sic_dock::scores
• CBScore_dist_score() : protocols::sic_dock
• CCD() : protocols::loops::loop_mover
• ccd_close_loops() : protocols::loops
• CD() : protocols::sic_dock::scores
• cdr_backbone_rmsds() : protocols::antibody
• cdr_CN_anchor_distance() : protocols::antibody
• cdr_energy() : protocols::antibody
• CDR_H3_cter_filter() : protocols::antibody
• CDR_H3_filter_legacy_code_with_old_rule() : protocols::antibody
• cdr_has_res_constraints() : protocols::antibody::constraints
• center_of_geom() : protocols::sic_dock
• center_of_mass() : core::pose , protocols::geometry
• center_residues() : protocols::cluster::calibur
• CENTROID() : core::chemical
• centroid_by_chain() : protocols::geometry
• centroid_by_chains() : protocols::geometry
• centroid_by_residues() : protocols::geometry
• centroid_dist() : protocols::toolbox::sample_around
• centroid_pair_by_jump() : protocols::geometry
• centroid_pose_from_pdb() : core::import_pose
• CENTROID_ROT() : core::chemical
• centroid_scatter() : core::scoring::fiber_diffraction
• CENTROID_WTS() : core::scoring
• centroids_by_jump() : protocols::geometry
• centroids_by_jump_int() : protocols::geometry
• CG() : protocols::sic_dock::scores
• chain_com() : protocols::membrane
• chain_end_res() : core::pose
• chain_gws_string() : core::io::carbohydrates
• chain_tm_com() : protocols::membrane
• CHAINBREAK_WEIGHT() : protocols::anchored_design
• change_cys_state() : core::conformation
• change_sheet_id_if_possible() : protocols::features::strand_assembly
• char_to_int() : core::io::carbohydrates
• char_valid_as_torsion_bin() : core::conformation
• character_is_USA_letter() : core::pose
• check_all_ligand_atoms() : protocols::ligand_docking::ligand_options
• check_all_residues_sampled() : core::pose::full_model_info
• check_and_correct_sister_atom_based_on_chirality() : core::io::pose_from_sfr
• check_and_correct_sister_atom_based_on_outgroup() : core::io::pose_from_sfr
• check_and_correct_sister_atoms() : core::io::pose_from_sfr
• check_base_pair() : protocols::rna::denovo
• check_base_pair_step_availability() : core::import_pose::libraries
• check_binary_chars() : core::io::serialization
• check_binary_unsigned_int() : core::io::serialization
• check_can_append() : protocols::stepwise::legacy::modeler::rna
• check_can_prepend() : protocols::stepwise::legacy::modeler::rna
• check_canonicalness_of_LR() : protocols::features::strand_assembly
• check_canonicalness_of_PA() : protocols::features::strand_assembly
• check_canonicalness_of_parallel_EE() : protocols::features::strand_assembly
• check_cb() : protocols::antibody::design
• check_deprecated_flags() : core::init
• check_extra_minimize_res_are_input() : core::import_pose
• check_fix_aho_cdr_numbering() : protocols::antibody
• check_for_connections_for_all_submotif_residues() : protocols::stepwise::monte_carlo::mover
• check_for_input_domain() : protocols::stepwise::modeler
• check_for_messed_up_structure() : protocols::stepwise::modeler::rna
• check_full_model_info_OK() : core::pose::full_model_info
• check_good_cutpoint_neighbour() : core::conformation
• check_good_neighbor() : core::conformation
• check_heading_direction() : protocols::features::strand_assembly
• check_helix_existence() : protocols::features::strand_assembly
• check_if_applicable() : core::chemical::carbohydrates
• check_if_pose_renumbered_for_clusters() : protocols::antibody::clusters
• check_if_proton_chi_atom() : protocols::simple_moves , protocols::stepwise::modeler::polar_hydrogens
• check_in_base_pair_list() : core::pose::rna
• check_instantiated_O2Prime_hydrogen() : protocols::stepwise::modeler::rna
• check_internal_hbonds() : protocols::fldsgn::topology
• check_is_working_res() : protocols::stepwise::modeler::rna
• check_jump_to_next_residue_in_chain() : protocols::stepwise::modeler
• check_jump_to_previous_residue_in_chain() : protocols::stepwise::modeler
• check_kink_helix() : protocols::fldsgn::topology
• check_load_fconfig() : core::init
• check_LR() : protocols::features::strand_assembly
• check_mutants_ok() : protocols::relax::membrane
• check_neighbor_ligand_atom() : protocols::ligand_docking::ligand_options
• check_o2prime_contact() : protocols::stepwise::modeler::packer
• check_orientation() : protocols::membrane
• check_PA() : protocols::features::strand_assembly
• check_phosphate_contacts_donor() : core::pose::rna
• check_required() : protocols::star
• check_required_cm() : protocols::medal
• check_required_common() : protocols::medal
• check_residue() : protocols::denovo_design::components
• check_residue_has_atom() : core::chemical
• check_residue_subset() : protocols::denovo_design::components
• check_RMSD() : protocols::ligand_docking
• check_rna_loop() : core::scoring::rna
• check_sample_sugar_in_full_model_info() : core::pose::full_model_info
• check_score() : protocols::ligand_docking
• check_score_function_sanity() : core::scoring
• check_scorefxn_has_constraint_terms_if_pose_has_constraints() : protocols::stepwise::modeler
• check_scores_from_parts() : protocols::stepwise::modeler
• check_stack() : core::scoring::rna
• check_strand_too_closeness() : protocols::features::strand_assembly
• check_surface_area_leerichards_deriv() : core::scoring::packstat
• check_sw_by_dis() : protocols::features::strand_assembly
• check_validity_and_get_working_res() : protocols::stepwise::modeler::rna
• check_vector() : protocols::membrane
• check_watson_crick_sequence() : core::scoring::rna
• check_whether_hairpin_connects_short_strand() : protocols::features::strand_assembly
• check_whether_same_direction_strands_connect_two_sheets_or_a_loop() : protocols::features::strand_assembly
• check_whether_sheets_are_connected_with_near_bb_atoms() : protocols::features::strand_assembly
• check_whether_strand_i_is_in_sheet() : protocols::features::strand_assembly
• check_whether_sw_by_sh_id_still_alive() : protocols::features::strand_assembly
• check_whether_sw_is_not_connected_with_continuous_atoms() : protocols::features::strand_assembly
• check_whether_this_pdb_should_be_excluded() : protocols::features::strand_assembly
• check_whether_this_sheet_is_too_short() : protocols::features::strand_assembly
• check_working_res() : core::import_pose
• checkpoint_cleanup() : protocols::dna
• checkpoint_with_interval() : protocols::checkpoint
• 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
• chiral1() : protocols::sic_dock::scores
• chiral2() : protocols::sic_dock::scores
• chiral3() : protocols::sic_dock::scores
• chiral4() : protocols::sic_dock::scores
• chis_from_pose() : protocols::comparative_modeling
• choose_canonical() : protocols::denovo_design::components
• choose_effective_sequence_separation() : core::scoring::constraints
• choose_hbond_parameter_set() : protocols::simple_pose_metric_calculators
• choose_random_if_unspecified_nucleotide() : protocols::stepwise::modeler::rna
• choose_randomly_from_allowed_at_position() : protocols::stepwise::modeler::rna
• chop_fragments() : core::fragment
• chr_chains() : core::chemical , core::conformation::symmetry
• chunk_library_inputter_xsd_type_definition_w_attributes() : protocols::jd3::chunk_library_inputters
• chunk_probabilities() : protocols::medal
• chunks_by_CA_CA_distance() : protocols::nonlocal
• cis_omega_torsion_bin() : core::conformation
• classify_base_pairs() : core::pose::rna
• classify_base_pairs_lores() : protocols::rna::denovo
• clean_for_storage() : protocols::denovo_design::components
• clean_from_storage() : protocols::denovo_design::components
• clean_res_list() : protocols::rna::movers
• clean_up_dangling_connect() : core::chemical
• cleanup() : core::import_pose
• clear_conformation_viewers() : protocols::viewer
• clear_rna_scoring_info() : core::scoring::rna
• clear_rna_secstruct_legacy_info() : core::pose::rna::secstruct_legacy
• clear_sm_data() : core::simple_metrics
• clearPoseExtraScore() : core::pose
• clearPoseExtraScores() : core::pose
• clockwise() : core::membrane
• 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 , protocols::matdes
• cmp_pair_by_second() : protocols::design_opt , protocols::matdes
• cmp_pair_vec_by_first_vec_val() : protocols::design_opt , protocols::matdes
• cmp_particles() : core::optimization
• cnl_com() : protocols::constel
• COARSE_RNA() : core::chemical
• codon2aa() : core::chemical::NucleotideTools
• collect_dofs() : protocols::environment
• com() : protocols::membrane
• com_calc() : protocols::environment
• com_of_true_residues() : protocols::rna::movers
• combinable() : core::scoring::constraints
• combine_and_trim() : protocols::nonlocal
• combine_constraints() : core::scoring::constraints
• combine_loops() : protocols::medal
• combine_movemaps_post_insertion() : protocols::grafting
• combine_NMR_atom_string() : core::scoring::constraints
• combine_sequence_mappings() : core::id
• combine_two_poses() : protocols::seeded_abinitio
• comma_separated_partner_chains() : protocols::docking
• 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
• common_movemap_complex_type_def() : protocols::rosetta_scripts
• common_setup() : protocols::abinitio
• compact_enum_set() : core::chemical::gasteiger
• compare() : protocols::fldsgn::topology , protocols::splice
• compare_atom_coordinates() : core::pose
• compare_atom_icoor() : core::chemical
• compare_binary_protein_silent_struct() : core::pose
• compare_by_abs() : core::scoring
• compare_mingraph_and_energy_graph() : core::pack
• compare_motif2scaffold_data_by_scaffold_low2high() : protocols::motif_grafting::movers
• compare_residue_connection() : core::chemical
• compare_RNA_char() : core::import_pose
• compare_RNA_secstruct() : core::import_pose
• compare_sequence_claim_priority() : protocols::topology_broker
• 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
• complex_ring_detection() : core::chemical
• complex_type_name_for_cluster_metric() : protocols::multistage_rosetta_scripts::cluster
• complex_type_name_for_features_reporter() : protocols::features
• complex_type_name_for_filter() : protocols::filters
• complex_type_name_for_jump_selector() : core::select::jump_selector
• complex_type_name_for_loop_definer() : protocols::loops::loops_definers
• complex_type_name_for_mover() : protocols::moves
• complex_type_name_for_packer_palette() : core::pack::palette
• complex_type_name_for_parsed_protocol_subelement() : protocols::rosetta_scripts
• complex_type_name_for_res_filter() : core::pack::task::operation
• complex_type_name_for_res_lvl_task_op() : core::pack::task::operation
• complex_type_name_for_residue_selector() : core::select::residue_selector
• complex_type_name_for_scoring_grid() : protocols::qsar::scoring_grid
• complex_type_name_for_simple_metric() : core::simple_metrics
• complex_type_name_for_subsubtag() : protocols::splice
• complex_type_name_for_subtag() : protocols::splice
• complex_type_name_for_task_op() : core::pack::task::operation
• compute_alt_weights_for_npd_hbonds() : core::pack::interaction_graph
• compute_atom_packing_scores() : core::scoring::packstat
• compute_avge_scores() : protocols::sasa_scores
• compute_bb_centroid() : core::scoring
• compute_bb_radius() : core::scoring
• compute_bulges() : protocols::fldsgn::topology
• compute_cav_ball_clusters() : core::scoring::packstat
• compute_cav_ball_neighbor_count() : core::scoring::packstat
• compute_cav_ball_volumes() : core::scoring::packstat
• compute_center_of_mass() : protocols::forge::remodel
• compute_chain_beginnings() : protocols::denovo_design::components
• compute_coefficients3() : core::scoring::electron_density::SplineInterp
• compute_coefficients4() : core::scoring::electron_density::SplineInterp
• compute_cutpoints() : protocols::denovo_design::components
• compute_dec15_score() : core::scoring::packing
• compute_embeddings_by_chain() : protocols::membrane
• compute_exact_geosol() : core::scoring::geometric_solvation
• compute_hnq_atoms() : protocols::constraint_generator
• 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_max_probability() : protocols::calc_taskop_filters
• compute_max_strand() : protocols::fldsgn::filters
• compute_mean_probability() : protocols::calc_taskop_filters
• compute_min_probability() : protocols::calc_taskop_filters
• compute_nres_in_asymmetric_unit() : protocols::constraint_generator
• 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_probability() : protocols::calc_taskop_filters
• compute_rdf_tracer() : protocols::ligand_docking
• compute_ref_atom() : protocols::constraint_generator
• compute_residue_packing_score() : core::scoring::packstat
• compute_residue_packing_scores() : core::scoring::packstat
• compute_residue_sasas_for_sasa_scores() : protocols::sasa_scores
• compute_residues_from_selectors() : protocols::denovo_design::movers
• compute_rmsd() : protocols::pose_metric_calculators
• 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_single_direction_deviation() : protocols::loops::loop_closure::ccd
• compute_smooth_nb_deriv() : core::scoring::packing
• compute_ss_regions() : protocols::loops
• compute_structure_based_embedding() : protocols::membrane
• compute_surface_area_leerichards() : core::scoring::packstat
• compute_surface_area_leerichards_deriv() : core::scoring::packstat
• compute_surrounding_sasa() : core::scoring::packstat
• compute_unique_chains() : core::pose
• concatenate_profiles() : protocols::splice
• concave_hull() : core::membrane
• concave_shell() : core::membrane
• conf2pdb_chain() : core::pose
• conf2pdb_chain_default_map() : core::pose
• configure_rmc() : protocols::star
• conj_map_times() : core::scoring::electron_density
• 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_full_model_info() : core::pose::full_model_info
• const_vdw_cached_rep_screen_info_from_pose() : protocols::scoring
• constrain_ligand_torsions() : protocols::ligand_docking
• constrain_pose_res_to_invrots() : protocols::toolbox::match_enzdes_util
• constrain_residue() : protocols::mpi_refinement
• constrain_ring_atoms() : core::pose::ncbb
• constraint_set_slice() : protocols::stepwise::modeler
• constraints_NtoC() : protocols::flxbb
• constraints_sheet() : protocols::flxbb
• construct_dummy_pose() : protocols::denovo_design
• construct_poly_ala_pose() : protocols::denovo_design , protocols::toolbox::pose_manipulation
• construct_poly_beta_ala_pose() : protocols::toolbox::pose_manipulation
• construct_poly_d_ala_pose() : protocols::toolbox::pose_manipulation
• construct_poly_d_beta_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::stepwise::modeler::rna
• Contain_seq_num() : core::scoring::rna::chemical_shift
• contains() : protocols::sparta
• Contains() : protocols::toolbox
• contains_protein() : protocols::stepwise::modeler::protein
• contains_stageid() : protocols::abinitio
• convert_acgu_to_1234() : core::chemical::rna
• convert_atom_name() : core::io::pose_from_sfr
• convert_based_on_match_type() : core::import_pose
• convert_binary_checkpoint() : protocols::frag_picker
• convert_cartesian_to_grid() : protocols::pockets
• convert_cartesian_to_spherical_coor_triplet() : protocols::pockets
• convert_from_std_map() : core::pose
• convert_grid_to_cartesian() : protocols::pockets
• convert_inorder_table_to_original_order() : core::scoring::trie
• convert_inorder_vector_to_original_order() : core::scoring::trie
• convert_na_to_1234() : core::scoring::rna
• convert_pre_spin_type_to_string() : core::scoring::nmr
• convert_rdc_type_to_string() : core::scoring::nmr
• convert_res_name() : core::io::pose_from_sfr
• convert_residue_names_into_linkage_map_key() : core::chemical::carbohydrates
• convert_residuetype_to_light_graph() : core::chemical
• convert_spherical_coor_triplet_to_cartesian() : protocols::pockets
• convert_string_to_averaging_type() : core::scoring::nmr
• convert_string_to_normalization_type() : core::scoring::nmr
• convert_string_to_rate_type() : core::scoring::nmr
• convert_string_to_weighting_scheme() : core::scoring::nmr
• convert_sugar_modeling_to_residue_alternative_set() : protocols::stepwise::modeler::rna::sugar
• convert_to_BondName() : core::chemical
• convert_to_fasta() : core::sequence
• convert_to_ResidueType() : core::chemical::sdf
• convert_to_ResidueTypes() : core::chemical::sdf
• convert_to_vector1() : protocols::stepwise::legacy::modeler::protein
• convert_to_working_res() : protocols::stepwise::legacy::modeler::protein
• ConvertToInterpolationCoefficients() : core::scoring::electron_density::SplineInterp
• convex_hull() : core::membrane
• convolute_maps() : core::scoring::electron_density
• coordinate_constrain_selection() : protocols::relax
• coords() : protocols::simple_filters , protocols::splice
• copy_all_o2prime_torsions() : protocols::stepwise::modeler::rna
• copy_bulge_res_and_sugar_torsion() : protocols::stepwise::modeler::rna::sugar
• copy_dofs() : core::pose::copydofs
• copy_dofs_match_atom_names() : core::pose::copydofs
• copy_dofs_sort_criterion() : protocols::stepwise::modeler::rna
• copy_helix_bondangles() : protocols::helical_bundle
• copy_helix_bondlengths() : protocols::helical_bundle
• copy_helix_dihedrals() : protocols::helical_bundle
• copy_hotspot_to_pose() : protocols::protein_interface_design::movers
• copy_internal_coords() : protocols::topology_broker
• copy_loop_pose_to_original() : protocols::generalized_kinematic_closure
• copy_over_phosphate_variants() : protocols::stepwise::modeler::rna::phosphate
• copy_pose_crd() : protocols::mpi_refinement
• copy_residue_coordinates_and_rebuild_missing_atoms() : core::conformation
• copy_residues() : protocols::star
• copy_side_chains() : protocols::abinitio
• correct_conn() : core::chemical
• correct_polymer_dependent_atoms_in_pose_segment() : protocols::generalized_kinematic_closure
• correctly_add_2prime_connection_variants() : core::pose
• correctly_add_cutpoint_variants() : core::pose
• correctly_remove_variants_incompatible_with_lower_cutpoint_variant() : core::pose
• correctly_remove_variants_incompatible_with_upper_cutpoint_variant() : core::pose
• count_AA_w_direction() : protocols::features::strand_assembly
• count_AA_wo_direction() : protocols::features::strand_assembly
• count_atom() : core::scoring::methods
• count_bulges() : protocols::denovo_design::components , protocols::denovo_design
• 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_neighbors() : protocols::ligand_docking::ga_ligand_dock
• count_neighbors_on_coord() : protocols::ligand_docking::ga_ligand_dock
• count_pair_bs() : core::scoring::methods
• count_selected() : core::select::residue_selector
• count_uniq_char() : protocols::ncbb
• counting_atoms_in_residue() : protocols::pockets
• covalent_compliance() : protocols::noesy_assign
• create_acc_orientation_vector() : core::scoring::hbonds
• create_adduct_combinations() : core::chemical
• create_alignment_id_map_legacy() : protocols::stepwise::modeler::align , protocols::stepwise::modeler::rna
• create_alpha_beta_models_table() : protocols::legacy_sewing
• create_and_init_hbond_graph() : core::pack::hbonds
• create_bond_length() : core::chemical
• create_cache() : protocols::frag_picker::scores
• create_chemical_edge() : core::pose
• create_command_map() : core::pack::task
• create_constel_records_from_sfr() : protocols::constel
• create_cpdata_correspondence_for_rotamer() : core::scoring::trie
• create_cpdata_correspondence_for_rotamerset() : core::scoring::trie
• create_don_orientation_vector() : core::scoring::hbonds
• create_entity_resfile_contents() : protocols::pack_daemon
• create_euler_rotation() : protocols::toolbox::rigid_body
• create_ExactSHOEnergy_from_cmdline() : core::scoring::geometric_solvation
• create_extra_output() : protocols::chemically_conjugated_docking , protocols::floppy_tail
• create_fasta_file() : core::sequence
• create_fragment_set() : protocols::hybridization
• create_fragment_set_no_ssbias() : protocols::hybridization
• create_full_to_input_res_map() : protocols::stepwise::modeler::rna
• create_func() : protocols::constraint_generator
• create_glycan_movemap_from_residue_selector() : core::pose::carbohydrates
• create_hbonds_one_way() : core::pack::interaction_graph
• create_ignore_list() : protocols::tcr
• create_init_and_create_edges_for_hbond_graph() : core::pack::hbonds
• create_long_range_energy_container() : core::scoring::methods
• create_map_for_Blosum62Map() : core::sequence
• create_match_position_modifier() : protocols::match
• create_membrane_docking_foldtree_from_partners() : protocols::membrane
• create_membrane_foldtree_anchor_com() : protocols::membrane
• create_membrane_foldtree_anchor_pose_tmcom() : protocols::membrane
• create_membrane_foldtree_anchor_tmcom() : protocols::membrane
• create_membrane_foldtree_from_anchors() : protocols::membrane
• create_membrane_multi_partner_foldtree_anchor_tmcom() : protocols::membrane
• create_minimization_graph() : core::pack
• create_model_from_pose() : protocols::legacy_sewing
• create_oriented_water_rotamer() : core::pack::rotamer_set
• create_packer_graph() : core::pack
• create_pdb_contents_from_sfr() : core::io::pdb
• create_pdb_info_for_single_residue_pose() : core::io::pdb
• create_pdb_line_from_record() : core::io::pdb
• create_record_from_pdb_line() : core::io::pdb
• create_records_from_pdb_file_contents() : core::io::pdb
• create_records_from_pdb_lines() : core::io::pdb
• create_records_from_sfr() : core::io::pdb
• create_remark_headers_from_cstcache() : protocols::enzdes::enzutil
• create_rna_vall_torsions() : protocols::rna::denovo
• create_rotamer_descriptor() : core::scoring::elec , core::scoring::hbonds , core::scoring::lkball
• create_rotamer_string() : protocols::stepwise::modeler::rna
• create_sasa_method() : core::scoring::sasa
• create_scmin_minimizer_map() : core::pack
• create_scorefxn() : protocols::stepwise::legacy::modeler::rna
• create_sequons() : protocols::carbohydrates
• create_sfr_from_cif_file_op() : core::io::mmcif
• create_sfr_from_mmtf_filename() : core::io::mmtf
• create_sfr_from_pdb_file_contents() : core::io::pdb
• create_sfr_from_pdb_records() : core::io::pdb
• create_sfrs_from_mmtf_filename() : core::io::mmtf
• create_shuffle_map_recursive_rms() : core::scoring
• create_specific_membrane_foldtree() : protocols::membrane
• create_standard_o2prime_pack_task() : protocols::stepwise::modeler::rna
• create_strand_list() : protocols::stepwise::modeler::rna
• create_subpose() : core::pose
• create_tag() : protocols::stepwise::modeler::rna
• create_torsion_value_string() : protocols::stepwise::modeler::rna
• create_trie() : core::scoring::trie
• create_working_data() : core::io::pose_from_sfr
• crossover() : protocols::ligand_docking::ga_ligand_dock
• crossover_ft() : protocols::ligand_docking::ga_ligand_dock
• crystRMS() : protocols::cryst
• crystRMSfast() : protocols::cryst
• cst_eq() : core::scoring::constraints
• cst_residue_in_pose() : protocols::toolbox::match_enzdes_util
• csv_to_container() : protocols::denovo_design
• ctname_for_pose_resource_loader() : core::import_pose
• ctrl_str_selector() : protocols::environment
• cubic_roots1() : protocols::cluster::calibur
• cubic_roots2() : protocols::cluster::calibur
• cull_violators() : core::scoring::constraints
• current_batch() : protocols::jd2
• current_batch_id() : protocols::jd2
• current_input_tag() : protocols::jd2
• current_nstruct_index() : protocols::jd2
• current_output_filename() : protocols::jd2
• current_output_name() : protocols::jd2
• current_replica() : protocols::jd2
• cutpoint_probabilities() : protocols::medal
• cutpoint_separation() : protocols::antibody
• cutpoints_separation() : protocols::antibody
• cyclize_pose() : protocols::relax