- c -

• c2_linker_dist : basic::options::OptionKeys::willmatch
• c2_symm_increment : basic::options::OptionKeys::willmatch
• c_cyd_seqpos : basic::options::OptionKeys::DisulfideInsertion
• C_root : basic::options::OptionKeys::FloppyTail
• ca_cb_clash_weight : basic::options::OptionKeys::mh::score
• ca_csts_dev : basic::options::OptionKeys::fold_from_loops
• Ca_Irms : basic::options::OptionKeys::evaluation
• ca_mask : basic::options::OptionKeys::edensity
• CA_MODEL : clean_pdb_keep_ligand
• ca_ratio : basic::options::OptionKeys::loodo
• ca_rmsd_cutoff : basic::options::OptionKeys::fold_from_loops
• CA_xyz : test::Workshop2test
• calc_pka : basic::options::OptionKeys::pH::calc_pka
• calc_rms_res : basic::options::OptionKeys::full_model
• calc_rot_boltz : basic::options::OptionKeys::matdes::mutalyze
• calc_sasa : basic::options::OptionKeys::pepspec
• calcenergy : basic::options::OptionKeys::pb_potential
• calcium_motif_score_weight : basic::options::OptionKeys::legacy_sewing
• call_back_function_body_template : binder
• calls : basic
• cam_shifts : basic::options::OptionKeys::evaluation
• camelid : basic::options::OptionKeys::antibody
• camelid_constraints : basic::options::OptionKeys::antibody
• canonical_sampling : basic::options::OptionKeys::canonical_sampling
• cap : basic::options::OptionKeys::loodo
• cap_e_potential : basic::options::OptionKeys::fingerprint
• caphit_rt_file : basic::options::OptionKeys::loodo
• carbohydrates : basic::options::OptionKeys::carbohydrates
• cart_min : basic::options::OptionKeys::stepwise::protein
• cartesian : basic::options::OptionKeys::ddg , basic::options::OptionKeys::relax
• cartesian_relax_rounds : basic::options::OptionKeys::cyclic_peptide
• cartmin : basic::options::OptionKeys::carbohydrates::glycan_sampler
• casp : basic::options::OptionKeys::casp
• category : pyrosetta::utility::array
• cavity_burial_probe_radius : basic::options::OptionKeys::packstat
• cb_clash_distance : basic::options::OptionKeys::carbohydrates::clash_check
• cb_sasa_thresh : basic::options::OptionKeys::willmatch
• cbeta : basic::options::OptionKeys::remodel
• ccd : basic::options::OptionKeys::loops::ccd , test::Workshop8test
• ccd_close : basic::options::OptionKeys::stepwise::protein
• ccd_closure : basic::options::OptionKeys::loops , loops
• CD : pyrosetta
• cdr_definition : basic::options::OptionKeys::antibody
• cdr_instructions : basic::options::OptionKeys::antibody::design
• cdr_set_cache_limit : basic::options::OptionKeys::antibody::design
• cdrs : test::G201_Module_Structure
• cen_minimize : basic::options::OptionKeys::remodel
• cen_patch : basic::options::OptionKeys::loops
• cen_sfxn : basic::options::OptionKeys::remodel
• cen_weights : basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::loops
• cen_wts : basic::options::OptionKeys::pepspec
• cenpack : basic::options::OptionKeys::remodel
• cenrot : basic::options::OptionKeys::corrections::score
• cenrot_cutoff : basic::options::OptionKeys::packing
• center : basic::options::OptionKeys::mp::setup
• center_at_interface : basic::options::OptionKeys::docking
• center_delta : basic::options::OptionKeys::mp
• center_jumps_in_single_stranded : basic::options::OptionKeys::rna::denovo
• center_mag : basic::options::OptionKeys::membrane
• center_max_delta : basic::options::OptionKeys::membrane
• center_search : basic::options::OptionKeys::membrane
• center_search_cycles : basic::options::OptionKeys::mp
• center_start : basic::options::OptionKeys::mp
• central_relax_pdb_num : basic::options::OptionKeys::pocket_grid
• centroid : basic::options::OptionKeys::in::file , basic::options::OptionKeys::relax::centroid
• centroid_all_val : basic::options::OptionKeys::smhybrid
• centroid_density_mass : basic::options::OptionKeys::edensity , basic::options::OptionKeys::score::fiber_diffraction
• centroid_distance_scale_factor : basic::options::OptionKeys::frags::contacts
• centroid_input : basic::options::OptionKeys::in::file
• centroid_loop_mover : basic::options::OptionKeys::ufv
• centroid_mode : basic::options::OptionKeys::relax
• centroid_only : basic::options::OptionKeys::lh
• centroid_output : basic::options::OptionKeys::stepwise::protein
• centroid_refine : basic::options::OptionKeys::antibody
• centroid_rot : basic::options::OptionKeys::optE
• centroid_rot_min : basic::options::OptionKeys::optE
• centroid_score_diff_cut : basic::options::OptionKeys::stepwise::protein
• centroid_screen : basic::options::OptionKeys::stepwise::protein , basic::options::OptionKeys::stepwise::rna
• centroid_sfx : basic::options::OptionKeys::ufv
• centroid_sfx_patch : basic::options::OptionKeys::ufv
• centroid_weights : basic::options::OptionKeys::stepwise::protein
• cereal : pyrosetta::distributed::utility::pickle
• cerr : utility::io::oc
• cg_res_type : basic::options::OptionKeys::pepspec
• ch_o_bond_potential : basic::options::OptionKeys::corrections::score
• chain : basic::options::OptionKeys::run
• chain_break_tol : basic::options::OptionKeys::loops
• chain_connection : basic::options::OptionKeys::rna::denovo
• chain_normal_angle_max : basic::options::OptionKeys::mp
• chainbreak_bias : basic::options::OptionKeys::rigid
• chainbreak_max : basic::options::OptionKeys::fast_loops
• chainbreak_max_accept : basic::options::OptionKeys::loops
• chainbreak_weight : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::relax
• chainbreak_weight_stage1 : basic::options::OptionKeys::jumps
• chainbreak_weight_stage2 : basic::options::OptionKeys::jumps
• chainbreak_weight_stage3 : basic::options::OptionKeys::jumps
• chainbreak_weight_stage4 : basic::options::OptionKeys::jumps
• chainbreaks : basic::options::OptionKeys::smhybrid
• chainid : clean_pdb_keep_ligand
• chains : basic::options::OptionKeys::intf
• chains_to_cyclize : basic::options::OptionKeys::cyclization
• chains_to_ignore : basic::options::OptionKeys::cluster::energy_based_clustering
• change_lig : basic::options::OptionKeys::enzdes
• change_movemap : basic::options::OptionKeys::templates
• charged_chains : basic::options::OptionKeys::pb_potential
• chat : basic::options
• check_all_PDB_components : basic::options::OptionKeys::in::file
• check_cdr_chainbreaks : basic::options::OptionKeys::antibody
• check_cdr_pep_bond_geom : basic::options::OptionKeys::antibody
• check_chains : basic::options::OptionKeys::carbohydrates::clash_check
• check_rama_scores : basic::options::OptionKeys::loops::ccd
• check_scored_centroid : basic::options::OptionKeys::remodel
• 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 , basic::options::OptionKeys::remodel , basic::options::OptionKeys::run
• checkpoint_file : basic::options::OptionKeys::cyclic_peptide , basic::options::OptionKeys::jd2
• checkpoint_interval : basic::options::OptionKeys::run
• checkpoint_job_identifier : basic::options::OptionKeys::cyclic_peptide
• checkpointing_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• chemical : basic::options::OptionKeys::chemical , basic::options::OptionKeys::corrections::chemical , basic::options::OptionKeys::mistakes::chemical
• chemical_shifts : basic::options::OptionKeys::evaluation
• chemically_conjugated_docking : basic::options::OptionKeys::chemically_conjugated_docking
• chi1_increment : basic::options::OptionKeys::willmatch
• chi2_increment : basic::options::OptionKeys::willmatch
• chi_iterations : basic::options::OptionKeys::score::fiber_diffraction
• chi_list1 : erraser_analysis
• chi_list2 : erraser_analysis
• chi_min : basic::options::OptionKeys::enzdes
• chi_move : basic::options::OptionKeys::relax
• chi_stdev : basic::options::OptionKeys::recces::thermal_sampling
• childlist : basic::options::OptionKeys::evolution
• chilist : basic::options::OptionKeys::willmatch
• chirmsd : basic::options::OptionKeys::evaluation
• chm : test::T100_Basic
• chname : basic::options::OptionKeys::out
• choose_random : basic::options::OptionKeys::stepwise
• chtimestamp : basic::options::OptionKeys::out
• chunk : basic::options::OptionKeys::chunk
• chunks : basic::options::OptionKeys::nonlocal
• cif_extra_data_separate_file : basic::options::OptionKeys::out::file
• cin : utility::io::ic
• circle : test::Workshop9test
• circle2 : test::Workshop9test
• clash1 : erraser_analysis
• clash2 : erraser_analysis
• clash_check : basic::options::OptionKeys::carbohydrates::clash_check
• clash_cutoff : basic::options::OptionKeys::pepspec
• clash_dis : basic::options::OptionKeys::crossmatch , basic::options::OptionKeys::sicdock , basic::options::OptionKeys::willmatch
• clash_distance_cutoff : basic::options::OptionKeys::gen_pharmacophore
• classic : basic::options::OptionKeys::relax
• clean : basic::options::OptionKeys::cloud
• clear_bprots : basic::options::OptionKeys::motifs
• clear_csts : basic::options::OptionKeys::fold_from_loops
• clear_pose_cache : basic::options::OptionKeys::abinitio
• clock_factor : basic
• clog : utility::io::oc
• clone_atom_types : basic::options::OptionKeys::chemical
• close_chbrk : basic::options::OptionKeys::abinitio
• close_enough : basic::options::OptionKeys::motifs
• close_loops : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::rigid , basic::options::OptionKeys::rna::denovo
• close_loops_after_each_move : basic::options::OptionKeys::rna::denovo
• close_loops_by_idealizing : basic::options::OptionKeys::abinitio
• cloud : basic::options::OptionKeys::cloud
• cluster : basic::options::OptionKeys::cluster , basic::options::OptionKeys::hotspot
• cluster_by : basic::options::OptionKeys::cluster::energy_based_clustering
• cluster_by_all_atom_rmsd : basic::options::OptionKeys::stepwise::protein
• cluster_csts_stats_cutoff : basic::options::OptionKeys::antibody
• cluster_cutoff : basic::options::OptionKeys::corrections::water
• cluster_cyclic_permutations : basic::options::OptionKeys::cluster::energy_based_clustering
• cluster_min_volume : basic::options::OptionKeys::packstat
• cluster_on_entire_pose : basic::options::OptionKeys::remodel
• cluster_radius : basic::options::OptionKeys::cluster::energy_based_clustering , basic::options::OptionKeys::corrections::water , basic::options::OptionKeys::remodel
• cm : basic::options::OptionKeys::cm
• cmiles : basic::options::OptionKeys::cmiles
• cn_symmetry : basic::options::OptionKeys::score::fiber_diffraction
• cognate_partners : basic::options::OptionKeys::pH
• cognate_pdb : basic::options::OptionKeys::pH
• colonyE : basic::options::OptionKeys::hotspot
• COLOR_LIB : PyMOL-RosettaServer
• colors : test::T150_PyMOL_Integration
• com_in_grid : basic::options::OptionKeys::loodo
• COM_root : basic::options::OptionKeys::FloppyTail
• COM_sd : basic::options::OptionKeys::remodel
• COM_tolerance : basic::options::OptionKeys::remodel
• combine : basic::options::OptionKeys::constraints
• combine_exclude_region : basic::options::OptionKeys::constraints
• combine_helical_silent_file : basic::options::OptionKeys::stepwise::rna
• combine_long_loop_mode : basic::options::OptionKeys::stepwise::rna
• combine_rate : basic::options::OptionKeys::loops
• combine_statistics : basic::options::OptionKeys::evaluation
• combined_constraints : basic::options::OptionKeys::evaluation
• combined_constraints_column : basic::options::OptionKeys::evaluation
• commit : version
• commit_id : version
• compare_native : basic::options::OptionKeys::enzdes
• compare_residue_energies_all : local
• compare_residue_energies_mut : local
• completion_notify_frequency : basic::options::OptionKeys::archive
• component_weights : basic::options::OptionKeys::optE
• compress_job_results : basic::options::OptionKeys::jd3
• compute_mg_sol_for_hydrogens : basic::options::OptionKeys::score
• compute_total_dist_cst : basic::options::OptionKeys::constraints
• conc : basic::options::OptionKeys::score
• condor : basic::options::OptionKeys::run
• config : basic::options::OptionKeys::frags::scoring , basic::options::OptionKeys::templates
• connect_info_cutoff : basic::options::OptionKeys::inout
• connection_scheme : basic::options::OptionKeys::ufv::insert
• conrot : basic::options::OptionKeys::canonical_sampling::probabilities
• cons_design_data_source : basic::options::OptionKeys::task_operations
• conservative_framework_design : basic::options::OptionKeys::antibody::design
• consolidate_matches : basic::options::OptionKeys::match
• constant_logic_taskops_file : basic::options::OptionKeys::optE
• constant_seed : basic::options::OptionKeys::run
• constrain_cter : basic::options::OptionKeys::antibody
• constrain_P : basic::options::OptionKeys::rna::erraser
• constrain_relax_segments : basic::options::OptionKeys::relax
• constrain_relax_to_native_coords : basic::options::OptionKeys::relax
• constrain_relax_to_start_coords : basic::options::OptionKeys::relax
• constrain_rigid_segments : basic::options::OptionKeys::loops
• constrain_vlvh_qq : basic::options::OptionKeys::antibody
• constrain_weights : basic::options::OptionKeys::optE
• constraint_skip_rate : basic::options::OptionKeys::fold_cst
• constraint_weight : basic::options::OptionKeys::ddg , basic::options::OptionKeys::DisulfideInsertion , local
• constraints : basic::options::OptionKeys::constraints , basic::options::OptionKeys::evaluation
• constraints_column : basic::options::OptionKeys::evaluation
• constraints_from_link_records : basic::options::OptionKeys::in
• constraints_NtoC : basic::options::OptionKeys::flxbb
• constraints_sheet : basic::options::OptionKeys::flxbb
• constraints_sheet_include_cacb_pseudotorsion : basic::options::OptionKeys::flxbb
• constructor_template : binder
• constructor_with_trampoline_template : binder
• contact_cutoffE : basic::options::OptionKeys::pose_metrics
• contact_dis : basic::options::OptionKeys::sicdock
• contact_dist : basic::options::OptionKeys::matdes::design
• contact_map : basic::options::OptionKeys::evaluation
• contact_score : basic::options::OptionKeys::jumps
• contactMap : basic::options::OptionKeys::contactMap
• contacts : basic::options::OptionKeys::frags::contacts
• context_round : basic::options::OptionKeys::optE::rescore
• continue_until_none_missing : basic::options::OptionKeys::stepwise::monte_carlo
• convergence_check_frequency : basic::options::OptionKeys::mc
• convert_protein_CEN : basic::options::OptionKeys::rna::denovo
• coord_constrain_sidechains : basic::options::OptionKeys::relax
• coord_cst : basic::options::OptionKeys::loops
• coord_cst_all_atom : basic::options::OptionKeys::loopfcst
• coord_cst_stdev : basic::options::OptionKeys::relax
• coord_cst_weight : basic::options::OptionKeys::loopfcst
• coord_cst_weight_array : basic::options::OptionKeys::loopfcst
• coord_cst_width : basic::options::OptionKeys::relax
• coorderr : basic::options::OptionKeys::mh::filter
• copyright : conf
• core_cutoff : basic::options::OptionKeys::remodel
• coreAA : basic::options::OptionKeys::remodel
• correct : basic::options::OptionKeys::corrections
• correct_NH_length : basic::options::OptionKeys::rdc
• correct_sign : basic::options::OptionKeys::nmr::rdc
• corrected_geo : basic::options::OptionKeys::rna
• corrections : basic::options::OptionKeys::corrections
• cosbeta_increment : basic::options::OptionKeys::sample_around
• count : clean_pdb_keep_ligand
• count_pair_hybrid : basic::options::OptionKeys::score
• count_sc_hbonds : basic::options::OptionKeys::cyclic_peptide
• counter : demo::D060_Folding , demo::D100_Docking , demo::D110_DNA_interface , demo::D120_Ligand_interface
• coupled_moves : basic::options::OptionKeys::coupled_moves
• cout : utility::io::oc
• covalent_labeling_fa_input : basic::options::OptionKeys::score
• covalent_labeling_input : basic::options::OptionKeys::score
• coverage_pow : basic::options::OptionKeys::mh::score
• cp : basic::options::OptionKeys::cp
• cpp_python_operator_map : binder
• cpp_set : test::T040_Types
• cpu_frac : basic::options::OptionKeys::boinc
• cpu_run_time : basic::options::OptionKeys::boinc
• cpu_run_timeout : basic::options::OptionKeys::boinc
• create_db : basic::options::OptionKeys::lh
• create_from_secondary_structure : basic::options::OptionKeys::DenovoProteinDesign
• create_from_template_pdb : basic::options::OptionKeys::DenovoProteinDesign
• create_score_function : pyrosetta
• createdb_rms_cutoff : basic::options::OptionKeys::lh
• crossmatch : basic::options::OptionKeys::crossmatch
• cryoem_scatterers : basic::options::OptionKeys::edensity
• cryst : basic::options::OptionKeys::cryst
• crystal_refine : basic::options::OptionKeys::cryst
• csa : basic::options::OptionKeys::csa , basic::options::OptionKeys::in::file , basic::options::OptionKeys::stepwise::monte_carlo::csa
• csa_bank_size : basic::options::OptionKeys::stepwise::monte_carlo::csa
• csa_output_rounds : basic::options::OptionKeys::stepwise::monte_carlo::csa
• csa_rmsd : basic::options::OptionKeys::stepwise::monte_carlo::csa
• cst : basic::options::OptionKeys::templates::cst
• cst_design : basic::options::OptionKeys::enzdes
• cst_dist_cutoff : basic::options::OptionKeys::ddg
• cst_dock : basic::options::OptionKeys::enzdes
• cst_fa_file : basic::options::OptionKeys::constraints
• cst_fa_only : basic::options::OptionKeys::remodel
• cst_fa_weight : basic::options::OptionKeys::constraints
• cst_file : basic::options::OptionKeys::cluster::energy_based_clustering , basic::options::OptionKeys::constraints , test::G100_Functions_Input
• cst_gap : basic::options::OptionKeys::rna::denovo
• cst_min : basic::options::OptionKeys::enzdes
• cst_opt : basic::options::OptionKeys::enzdes
• cst_predock : basic::options::OptionKeys::enzdes
• cst_seqwidth : basic::options::OptionKeys::RBSegmentRelax
• cst_sub_files : basic::options::OptionKeys::smhybrid
• cst_weight : basic::options::OptionKeys::constraints
• cst_weight_coord : basic::options::OptionKeys::cm::sanitize
• cst_weight_pair : basic::options::OptionKeys::cm::sanitize
• cstfile : basic::options::OptionKeys::enzdes , basic::options::OptionKeys::remodel
• cstfilter : basic::options::OptionKeys::remodel
• cter_insert : basic::options::OptionKeys::antibody
• Ctermini : basic::options::OptionKeys::in
• CubeSyms : basic::sampling::orientations
• cull_with_native : basic::options::OptionKeys::constraints
• current_chunk : rna_decompose
• custom_atom_pair : basic::options::OptionKeys::score
• custom_ff : basic::options::OptionKeys::score::saxs
• cut1 : basic::options::OptionKeys::enzdes
• cut2 : basic::options::OptionKeys::enzdes
• cut3 : basic::options::OptionKeys::enzdes
• cut4 : basic::options::OptionKeys::enzdes
• cut_at_rna_chainbreak : basic::options::OptionKeys::rna
• cutoff : basic::options::OptionKeys::cp
• cutoutdomain : basic::options::OptionKeys::cutoutdomain
• cutpoint : loops
• cutpoint_closed : basic::options::OptionKeys::full_model
• cutpoint_open : basic::options::OptionKeys::full_model
• cycle_ratio : basic::options::OptionKeys::relax
• cycles : basic::options::OptionKeys::magnesium::montecarlo , basic::options::OptionKeys::relax::range , basic::options::OptionKeys::rna::denovo , basic::options::OptionKeys::stepwise::monte_carlo , demo::D060_Folding , demo::D070_Refinement
• cycles_inner : basic::options::OptionKeys::run
• cycles_outer : basic::options::OptionKeys::run
• cyclic : basic::options::OptionKeys::cluster::energy_based_clustering , peptoid_design
• cyclic_peptide : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::cyclic_peptide , basic::options::OptionKeys::relax , basic::options::OptionKeys::remodel::RemodelLoopMover
• cyclic_permutation_offset : basic::options::OptionKeys::cluster::energy_based_clustering
• cyclic_permutations : basic::options::OptionKeys::cyclic_peptide
• cyclic_symmetry : basic::options::OptionKeys::cluster::energy_based_clustering
• cyclic_symmetry_mirroring : basic::options::OptionKeys::cluster::energy_based_clustering
• cyclic_symmetry_threshold : basic::options::OptionKeys::cluster::energy_based_clustering
• cyclization : basic::options::OptionKeys::cyclization
• cyclization_type : basic::options::OptionKeys::cyclic_peptide
• cyclize : basic::options::OptionKeys::full_model
• cys_prob : basic::options::OptionKeys::blivens::disulfide_scorer