- c -

• c2_linker_dist() : willmatch
• c2_symm_increment() : willmatch
• C_root() : basic::options::OptionKeys::FloppyTail , FloppyTail
• ca_csts_dev() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• Ca_Irms() : basic::options::OptionKeys::evaluation , evaluation
• ca_mask() : basic::options::OptionKeys::edensity , edensity
• ca_rmsd_cutoff() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• CA_tether() : basic::options::OptionKeys::constraints , constraints
• calc_pka() : pH::calc_pka
• calc_quadratic() : basic
• calc_rms() : numeric::model_quality
• calc_rms_fast() : numeric::model_quality
• calc_rms_res() : basic::options::OptionKeys::full_model , full_model
• calc_rot_boltz() : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• calc_sasa() : pepspec
• calcenergy() : pb_potential
• cam_shifts() : basic::options::OptionKeys::evaluation , evaluation
• camelid() : antibody , basic::options::OptionKeys::antibody
• camelid_constraints() : antibody , basic::options::OptionKeys::antibody
• canonical_sampling() : basic::options::OptionKeys::canonical_sampling , canonical_sampling
• cap_rot_cst_enrg() : basic::options::OptionKeys::ddg , ddg
• carbohydrates() : basic::options::OptionKeys::carbohydrates , carbohydrates
• cart_min() : stepwise::protein
• cartesian() : relax
• CASE_SENSITIVE() : platform::file
• casp() : basic::options::OptionKeys::casp , casp
• cav_shrink() : basic::options::OptionKeys::holes , holes
• cavity_burial_probe_radius() : packstat
• cb_sasa_thresh() : willmatch
• cbeta() : remodel
• ccd_close() : stepwise::protein
• ccd_closure() : basic::options::OptionKeys::loops , loops
• cdr_definition() : antibody , basic::options::OptionKeys::antibody
• cen_minimize() : remodel
• cen_patch() : basic::options::OptionKeys::loops , loops
• cen_sfxn() : remodel
• cen_weights() : basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::loops , FloppyTail , loops
• cen_wts() : pepspec
• cenpack() : remodel
• cenrot() : basic::options::OptionKeys::corrections::score , corrections::score
• cenrot_cutoff() : packing
• center() : numeric
• center_at_interface() : basic::options::OptionKeys::docking , docking
• center_atoms_at_origin() : numeric::model_quality
• center_mag() : basic::options::OptionKeys::membrane , membrane
• center_max_delta() : basic::options::OptionKeys::membrane , membrane
• center_of_mass() : numeric
• center_search() : basic::options::OptionKeys::membrane , membrane
• central_relax_pdb_num() : pocket_grid
• centroid() : basic::options::OptionKeys::in::file , in::file , relax::centroid
• centroid_all_val() : smhybrid
• centroid_density_mass() : basic::options::OptionKeys::edensity , edensity
• centroid_distance_scale_factor() : basic::options::OptionKeys::frags::contacts , frags::contacts
• centroid_input() : basic::options::OptionKeys::in::file , in::file
• centroid_loop_mover() : ufv
• centroid_mode() : relax
• centroid_only() : basic::options::OptionKeys::lh , lh
• centroid_output() : stepwise::protein
• centroid_refine() : antibody , basic::options::OptionKeys::antibody
• centroid_score_diff_cut() : stepwise::protein
• centroid_screen() : stepwise::protein , stepwise::rna
• centroid_sfx() : basic::options::OptionKeys::fldsgn , fldsgn , ufv
• centroid_sfx_patch() : basic::options::OptionKeys::fldsgn , fldsgn , ufv
• centroid_weights() : stepwise::protein
• cg_res_type() : pepspec
• ch_o_bond_potential() : basic::options::OptionKeys::corrections::score , corrections::score
• chain() : run
• chain_break_tol() : basic::options::OptionKeys::loops , loops
• chainbreak_bias() : rigid
• chainbreak_max() : basic::options::OptionKeys::fast_loops , fast_loops
• chainbreak_max_accept() : basic::options::OptionKeys::loops , loops
• chainbreak_weight() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , relax
• chainbreak_weight_stage1() : basic::options::OptionKeys::jumps , jumps
• chainbreak_weight_stage2() : basic::options::OptionKeys::jumps , jumps
• chainbreak_weight_stage3() : basic::options::OptionKeys::jumps , jumps
• chainbreak_weight_stage4() : basic::options::OptionKeys::jumps , jumps
• chainbreaks() : smhybrid
• chainParams() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• chainTORS() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• chainXYZ() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• change_lig() : basic::options::OptionKeys::enzdes , enzdes
• change_movemap() : templates
• char_equali() : utility::file
• charged_chains() : pb_potential
• chat() : basic::options
• check_cast() : basic
• check_scored_centroid() : remodel
• check_statement_sanity() : basic::database
• checkpoint() : basic::options::OptionKeys::dna::design , basic::options::OptionKeys::enzdes , basic::options::OptionKeys::fold_from_loops , basic::options::OptionKeys::in::file , basic::options::OptionKeys::ms::checkpoint , dna::design , enzdes , fold_from_loops , in::file , ms::checkpoint , remodel , run
• checkpoint_file() : basic::options::OptionKeys::jd2 , jd2
• checkpoint_interval() : run
• chemical() : basic::options::OptionKeys::chemical , basic::options::OptionKeys::corrections::chemical , basic::options::OptionKeys::mistakes::chemical , chemical , corrections::chemical , mistakes::chemical
• chemical_shifts() : basic::options::OptionKeys::evaluation , evaluation
• chemically_conjugated_docking() : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• chi1_increment() : willmatch
• chi2_increment() : willmatch
• chi_min() : basic::options::OptionKeys::enzdes , enzdes
• chi_move() : relax
• childlist() : basic::options::OptionKeys::evolution , evolution
• chilist() : willmatch
• chirmsd() : basic::options::OptionKeys::evaluation , evaluation
• chname() : out
• choose_random() : stepwise
• chrisk() : basic::options::OptionKeys::chrisk , chrisk
• chtimestamp() : out
• chunk() : basic::options::OptionKeys::chunk , chunk
• chunks() : basic::options::OptionKeys::nonlocal , nonlocal
• clamp() : numeric
• clash_cutoff() : pepspec
• clash_dis() : basic::options::OptionKeys::crossmatch , crossmatch , sicdock , willmatch
• classic() : relax
• clean() : run
• clear_bprots() : basic::options::OptionKeys::motifs , motifs
• clear_csts() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• clear_pose_cache() : abinitio , basic::options::OptionKeys::abinitio
• clock_factor() : basic
• close_chbrk() : abinitio , basic::options::OptionKeys::abinitio
• close_enough() : basic::options::OptionKeys::motifs , motifs , numeric::model_quality
• close_loops() : abinitio , basic::options::OptionKeys::abinitio , rigid
• close_loops_by_idealizing() : abinitio , basic::options::OptionKeys::abinitio
• closest_point_on_line() : numeric
• cluster() : basic::options::OptionKeys::cluster , basic::options::OptionKeys::hotspot , cluster , hotspot
• cluster_by_all_atom_rmsd() : stepwise::protein
• cluster_min_volume() : packstat
• cluster_on_entire_pose() : remodel
• cluster_radius() : remodel
• cm() : basic::options::OptionKeys::cm , cm
• cmiles() : basic::options::OptionKeys::cmiles , cmiles
• code_from_6bit() : utility
• code_to_6bit() : utility
• cognate_partners() : pH
• cognate_pdb() : pH
• collect_clustered_top() : remodel
• colonyE() : basic::options::OptionKeys::hotspot , hotspot
• COM_sd() : remodel
• COM_tolerance() : remodel
• COMAS() : numeric::model_quality
• combine() : basic::options::OptionKeys::constraints , constraints
• combine_exclude_region() : basic::options::OptionKeys::constraints , constraints
• combine_helical_silent_file() : stepwise::rna
• combine_long_loop_mode() : stepwise::rna
• combine_names() : utility::file
• combine_rate() : basic::options::OptionKeys::loops , loops
• combine_statistics() : basic::options::OptionKeys::evaluation , evaluation
• combined_constraints() : basic::options::OptionKeys::evaluation , evaluation
• combined_constraints_column() : basic::options::OptionKeys::evaluation , evaluation
• comma_seperated_string_to_xyz() : numeric
• comparable() : utility::keys
• compare_native() : basic::options::OptionKeys::enzdes , enzdes
• complete_link_clustering() : numeric
• completion_notify_frequency() : archive , basic::options::OptionKeys::archive
• component_weights() : basic::options::OptionKeys::optE , optE
• compute_total_dist_cst() : basic::options::OptionKeys::constraints , constraints
• conc() : score
• cond_exit() : utility
• condor() : run
• config() : basic::options::OptionKeys::frags::scoring , frags::scoring , templates
• connect_info_cutoff() : basic::options::OptionKeys::inout , inout
• connection_scheme() : ufv::insert
• conrot() : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• conservative_h3_design() : antibody::design , basic::options::OptionKeys::antibody::design
• consolidate_matches() : basic::options::OptionKeys::match , match
• const_pointer_cast() : utility::pointer
• constant_logic_taskops_file() : basic::options::OptionKeys::optE , optE
• constant_seed() : run
• constrain_cter() : antibody , basic::options::OptionKeys::antibody
• constrain_relax_segments() : relax
• constrain_relax_to_native_coords() : relax
• constrain_relax_to_start_coords() : relax
• constrain_rigid_segments() : basic::options::OptionKeys::loops , loops
• constrain_vlvh_qq() : antibody , basic::options::OptionKeys::antibody
• constrain_weights() : basic::options::OptionKeys::optE , optE
• constraint_max() : basic::options::OptionKeys::motifs , motifs
• constraint_skip_rate() : basic::options::OptionKeys::fold_cst , fold_cst
• constraint_weight() : basic::options::OptionKeys::ddg , ddg
• constraints() : basic::options::OptionKeys::constraints , basic::options::OptionKeys::evaluation , constraints , evaluation
• constraints_column() : basic::options::OptionKeys::evaluation , evaluation
• constraints_NtoC() : basic::options::OptionKeys::flxbb , flxbb
• constraints_sheet() : basic::options::OptionKeys::flxbb , flxbb
• constraints_sheet_include_cacb_pseudotorsion() : basic::options::OptionKeys::flxbb , flxbb
• construct_kd_tree() : numeric::kdtree
• contact_cutoffE() : pose_metrics
• contact_dis() : sicdock
• contact_dist() : basic::options::OptionKeys::matdes::design , matdes::design
• contact_map() : basic::options::OptionKeys::evaluation , evaluation
• contact_score() : basic::options::OptionKeys::jumps , jumps
• contactMap() : basic::options::OptionKeys::contactMap , contactMap
• contacts() : basic::options::OptionKeys::frags::contacts , frags::contacts
• context_round() : basic::options::OptionKeys::optE::rescore , optE::rescore
• convergence_check_frequency() : basic::options::OptionKeys::mc , mc
• coord_constrain_sidechains() : relax
• coord_cst() : basic::options::OptionKeys::loops , loops
• coord_cst_all_atom() : basic::options::OptionKeys::loopfcst , loopfcst
• coord_cst_stdev() : relax
• coord_cst_weight() : basic::options::OptionKeys::loopfcst , loopfcst
• coord_cst_weight_array() : basic::options::OptionKeys::loopfcst , loopfcst
• coord_cst_width() : relax
• coorderr() : basic::options::OptionKeys::mh::filter , mh::filter
• core_cutoff() : remodel
• corrcoef() : numeric::statistics
• corrcoef_with_provided_mean_and_std_dev() : numeric::statistics
• correct() : basic::options::OptionKeys::corrections , corrections
• correct_NH_length() : rdc
• corrected_geo() : rna
• corrections() : basic::options::OptionKeys::corrections , corrections
• cos_of() : numeric
• cot() : numeric
• cov() : numeric::statistics
• cov_with_provided_mean() : numeric::statistics
• cp() : basic::options::OptionKeys::cp , cp
• cpu_frac() : basic::options::OptionKeys::boinc , boinc
• cpu_run_time() : basic::options::OptionKeys::boinc , boinc
• cpu_run_timeout() : basic::options::OptionKeys::boinc , boinc
• create_add() : utility::query::metric_operators
• create_ander() : utility::query::filter_operators
• create_blank_file() : utility::file
• create_db() : basic::options::OptionKeys::lh , lh
• create_directory() : utility::file
• create_directory_recursive() : utility::file
• create_div() : utility::query::metric_operators
• create_eq() : utility::query::metric_operators
• create_from_secondary_structure() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• create_from_template_pdb() : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• create_gt() : utility::query::metric_operators
• create_gte() : utility::query::metric_operators
• create_lt() : utility::query::metric_operators
• create_lte() : utility::query::metric_operators
• create_mult() : utility::query::metric_operators
• create_neg() : utility::query::metric_operators
• create_neq() : utility::query::metric_operators
• create_noter() : utility::query::filter_operators
• create_orer() : utility::query::filter_operators
• create_pow() : utility::query::metric_operators
• create_sub() : utility::query::metric_operators
• createdb_rms_cutoff() : basic::options::OptionKeys::lh , lh
• createRG() : numeric::random
• cross() : numeric , numeric::kinematic_closure , numeric::kinematic_closure::radians
• cross_product() : numeric
• crossmatch() : basic::options::OptionKeys::crossmatch , crossmatch
• crossp() : numeric::kinematic_closure
• cryoem_scatterers() : basic::options::OptionKeys::edensity , edensity
• cryst() : basic::options::OptionKeys::cryst , cryst
• crystal_refine() : basic::options::OptionKeys::cryst , cryst
• csa() : basic::options::OptionKeys::csa , basic::options::OptionKeys::in::file , csa , in::file
• csc() : numeric
• cst() : templates::cst
• cst_design() : basic::options::OptionKeys::enzdes , enzdes
• cst_dock() : basic::options::OptionKeys::enzdes , enzdes
• cst_fa_file() : basic::options::OptionKeys::constraints , constraints
• cst_fa_weight() : basic::options::OptionKeys::constraints , constraints
• cst_file() : basic::options::OptionKeys::constraints , constraints
• cst_min() : basic::options::OptionKeys::enzdes , enzdes
• cst_opt() : basic::options::OptionKeys::enzdes , enzdes
• cst_pdb() : RBSegmentRelax
• cst_predock() : basic::options::OptionKeys::enzdes , enzdes
• cst_seqwidth() : RBSegmentRelax
• cst_sub_files() : smhybrid
• cst_weight() : basic::options::OptionKeys::constraints , constraints
• cst_weight_coord() : basic::options::OptionKeys::cm::sanitize , cm::sanitize
• cst_weight_pair() : basic::options::OptionKeys::cm::sanitize , cm::sanitize
• cst_width() : RBSegmentRelax
• cst_wt() : RBSegmentRelax
• cstfile() : basic::options::OptionKeys::enzdes , enzdes , remodel
• cstfilter() : remodel
• cter_insert() : antibody , basic::options::OptionKeys::antibody
• cterm_seq() : assembly , basic::options::OptionKeys::assembly
• Ctermini() : basic::options::OptionKeys::in , in
• cube() : numeric
• cull_with_native() : basic::options::OptionKeys::constraints , constraints
• cumulative() : numeric
• custom_atom_pair() : score
• custom_ff() : score::saxs
• cut1() : basic::options::OptionKeys::enzdes , enzdes
• cut2() : basic::options::OptionKeys::enzdes , enzdes
• cut3() : basic::options::OptionKeys::enzdes , enzdes
• cut4() : basic::options::OptionKeys::enzdes , enzdes
• cutoff() : basic::options::OptionKeys::cp , cp
• cutoutdomain() : basic::options::OptionKeys::cutoutdomain , cutoutdomain
• cutpoint_closed() : basic::options::OptionKeys::full_model , full_model
• cutpoint_open() : basic::options::OptionKeys::full_model , full_model
• cycle_ratio() : relax
• cycles() : stepwise::monte_carlo
• cycles_inner() : run
• cycles_outer() : run
• cyclic_peptide() : remodel::RemodelLoopMover
• cys_prob() : basic::options::OptionKeys::blivens::disulfide_scorer , blivens::disulfide_scorer