- c -

• Ca_coord() : protocols::simple_moves
• Ca_coords() : protocols::simple_moves
• 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_all_dist() : protocols::make_rot_lib
• calc_CA_Irmsd() : protocols::docking
• calc_centroids() : protocols::make_rot_lib
• calc_delta_sasa() : protocols::fldsgn::topology
• calc_dist() : protocols::make_rot_lib
• calc_fit_R() : protocols::toolbox
• calc_Fnat() : protocols::docking
• calc_Fnonnat() : protocols::docking
• calc_interaction_energy() : protocols::docking
• calc_Irmsd() : protocols::docking
• calc_Lrmsd() : protocols::docking
• calc_pareto_front() : protocols::design_opt , protocols::matdes
• calc_pareto_front_nbrs() : protocols::design_opt , protocols::matdes
• calc_per_residue_scores() : protocols::sparta
• calc_res_contact() : protocols::docking
• calc_rotamer_clusters() : protocols::make_rot_lib
• calc_rsd_sasa() : protocols::forge::methods
• calc_std_dev() : protocols::make_rot_lib
• calc_strand_pairing_set() : protocols::fldsgn::topology
• 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_dihedral_distance() : protocols::antibody::clusters
• calculate_dihedral_w_4_resnums() : protocols::features::strand_assembly
• calDist() : protocols::pockets
• canonical_sampling_main() : protocols::canonical_sampling
• catalytic_res() : protocols::enzdes::enzutil
• 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
• CBlocal() : protocols::sic_dock::scores
• CBScore_dist_score() : protocols::sic_dock
• CCD() : protocols::loops::loop_mover
• ccd_close_loops() : protocols::loops
• 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() : protocols::membrane::geometry
• centroid_dist() : protocols::toolbox::sample_around
• centroid_pair_by_jump() : protocols::geometry
• centroids_by_jump() : protocols::geometry
• centroids_by_jump_int() : protocols::geometry
• change_sheet_id_if_possible() : protocols::features::strand_assembly
• check_all_ligand_atoms() : protocols::ligand_docking::ligand_options
• check_base_pair() : protocols::farna
• 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_extra_minimize_res_are_input() : protocols::stepwise::setup
• check_for_input_domain() : protocols::stepwise::modeler
• check_for_messed_up_structure() : protocols::stepwise::modeler::rna
• check_heading_direction() : protocols::features::strand_assembly
• check_helix_existence() : protocols::features::strand_assembly
• 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() : protocols::farna
• 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_LR() : protocols::features::strand_assembly
• check_move_map_against_working_parameters() : protocols::stepwise::modeler::movemap
• check_neighbor_ligand_atom() : protocols::ligand_docking::ligand_options
• check_o2prime_contact() : protocols::stepwise::modeler::packer
• check_PA() : protocols::features::strand_assembly
• check_phosphate_contacts_donor() : protocols::stepwise::modeler::rna::phosphate
• 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::stepwise::modeler
• check_strand_too_closeness() : protocols::features::strand_assembly
• check_sw_by_dis() : protocols::features::strand_assembly
• check_validity_and_get_working_res() : protocols::stepwise::modeler::rna
• check_vector() : protocols::membrane::geometry
• 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() : protocols::stepwise::setup
• checkpoint_cleanup() : protocols::dna
• checkpoint_with_interval() : protocols::checkpoint
• 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_hbond_parameter_set() : protocols::toolbox::pose_metric_calculators
• choose_random_if_unspecified_nucleotide() : protocols::stepwise::modeler::rna
• chunk_probabilities() : protocols::medal
• chunks_by_CA_CA_distance() : protocols::nonlocal
• cleanup() : protocols::stepwise::setup
• clear_conformation_viewers() : protocols::viewer
• 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
• collect_dofs() : protocols::environment
• com_calc() : protocols::environment
• combine_and_trim() : protocols::nonlocal
• combine_loops() : protocols::medal
• combine_movemaps_post_insertion() : protocols::grafting
• combine_two_poses() : protocols::seeded_abinitio
• common_setup() : protocols::abinitio
• compare() : protocols::fldsgn::topology
• compare_motif2scaffold_data_by_scaffold_low2high() : protocols::motif_grafting::movers
• compare_RNA_char() : protocols::farna
• compare_RNA_secstruct() : protocols::farna
• compare_sequence_claim_priority() : protocols::topology_broker
• compareIndexEnergyPair() : protocols::cluster , protocols::toolbox
• compareRef_fxn() : protocols::sparta
• complete_connections_tracer() : protocols::ligand_docking
• compute_avge_scores() : protocols::sasa_scores
• compute_center_of_mass() : protocols::forge::remodel
• compute_per_residue_probabilities() : protocols::star
• compute_rdf_tracer() : protocols::ligand_docking
• compute_residue_sasas_for_sasa_scores() : protocols::sasa_scores
• compute_sasapack_scores() : protocols::sasa_scores
• compute_single_direction_deviation() : protocols::loops::loop_closure::ccd
• compute_ss_regions() : protocols::loops
• compute_structure_based_embedding() : protocols::membrane::geometry
• configure_rmc() : protocols::star
• connect_from() : protocols::protein_interface_design::movers
• connect_to() : protocols::protein_interface_design::movers
• connected_mainchain_atomids() : protocols::backrub
• connects_rigid_regions() : protocols::topology_broker
• constrain_ligand_torsions() : protocols::ligand_docking
• constrain_pose_res_to_invrots() : protocols::toolbox::match_enzdes_util
• constrain_residue() : protocols::mpi_refinement
• constraint_set_slice() : protocols::stepwise::modeler
• 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::stepwise::modeler::rna
• contains() : protocols::sparta
• Contains() : protocols::toolbox
• contains_protein() : protocols::stepwise::modeler::protein
• contains_stageid() : protocols::abinitio
• convert_based_on_match_type() : protocols::farna
• convert_cartesian_to_grid() : protocols::pockets
• convert_cartesian_to_spherical_coor_triplet() : protocols::pockets
• convert_grid_to_cartesian() : protocols::pockets
• Convert_rebuild_residue_string_to_list() : protocols::stepwise::modeler::rna
• convert_spherical_coor_triplet_to_cartesian() : protocols::pockets
• convert_sugar_modeling_to_residue_alternative_set() : protocols::stepwise::modeler::rna::sugar
• convert_to_vector1() : protocols::stepwise::legacy::modeler::protein
• convert_to_working_res() : protocols::stepwise::legacy::modeler::protein
• coordinate_constrain_selection() : protocols::relax
• coords() : protocols::simple_filters
• copy_all_o2prime_torsions() : protocols::stepwise::modeler::rna
• copy_bulge_res_and_sugar_torsion() : protocols::stepwise::modeler::rna::sugar
• 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_residues() : protocols::star
• copy_side_chains() : protocols::abinitio
• correctly_position_five_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate
• correctly_position_five_prime_phosphate_SLOW() : protocols::stepwise::modeler::rna::phosphate
• count_AA_w_direction() : protocols::features::strand_assembly
• count_AA_wo_direction() : protocols::features::strand_assembly
• count_buried_unsat_Hbonds() : protocols::ligand_docking
• count_CBs() : protocols::sic_dock
• count_cutpoints() : protocols::forge::methods
• count_linkers() : protocols::sic_dock
• covalent_compliance() : protocols::noesy_assign
• create_aligment_id_map_legacy() : protocols::stepwise::modeler::align , protocols::stepwise::modeler::rna
• create_cache() : protocols::frag_picker::scores
• create_entity_resfile_contents() : protocols::pack_daemon
• create_euler_rotation() : protocols::toolbox::rigid_body
• create_extra_output() : protocols::floppy_tail
• create_fragment_set() : protocols::hybridization
• create_fragment_set_no_ssbias() : protocols::hybridization
• create_full_to_input_res_map() : protocols::stepwise::modeler::rna
• create_match_position_modifier() : protocols::match
• create_remark_headers_from_cstcache() : protocols::enzdes::enzutil
• create_rna_vall_torsions() : protocols::farna
• create_rotamer_string() : protocols::stepwise::modeler::rna
• create_scorefxn() : protocols::stepwise::legacy::modeler::rna
• create_standard_o2prime_pack_task() : protocols::stepwise::modeler::rna
• create_strand_list() : protocols::stepwise::modeler::rna
• create_tag() : protocols::stepwise::modeler::rna
• create_torsion_value_string() : protocols::stepwise::modeler::rna
• cst_residue_in_pose() : protocols::toolbox::match_enzdes_util
• ctrl_str_selector() : protocols::environment
• current_batch() : protocols::jd2
• current_job() : protocols::nonlocal
• 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::forge::methods