- c -

c2_linker_dist : basic::options::OptionKeys::willmatch
c2_symm_increment : basic::options::OptionKeys::willmatch
C_root : basic::options::OptionKeys::FloppyTail
ca_csts_dev : basic::options::OptionKeys::fold_from_loops
Ca_Irms : basic::options::OptionKeys::evaluation
ca_mask : basic::options::OptionKeys::edensity
ca_rmsd_cutoff : basic::options::OptionKeys::fold_from_loops
CA_tether : basic::options::OptionKeys::constraints
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
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_rot_cst_enrg : basic::options::OptionKeys::ddg
carbohydrates : basic::options::OptionKeys::carbohydrates
cart_min : basic::options::OptionKeys::stepwise::protein
cartesian : basic::options::OptionKeys::relax
casp : basic::options::OptionKeys::casp
cav_shrink : basic::options::OptionKeys::holes
cavity_burial_probe_radius : basic::options::OptionKeys::packstat
cb_sasa_thresh : basic::options::OptionKeys::willmatch
cbeta : basic::options::OptionKeys::remodel
ccd_close : basic::options::OptionKeys::stepwise::protein
ccd_closure : basic::options::OptionKeys::loops
cdr_definition : basic::options::OptionKeys::antibody
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_at_interface : basic::options::OptionKeys::docking
center_mag : basic::options::OptionKeys::membrane
center_max_delta : basic::options::OptionKeys::membrane
center_search : basic::options::OptionKeys::membrane
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
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_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::fldsgn , basic::options::OptionKeys::ufv
centroid_sfx_patch : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::ufv
centroid_weights : basic::options::OptionKeys::stepwise::protein
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
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
change_lig : basic::options::OptionKeys::enzdes
change_movemap : basic::options::OptionKeys::templates
charged_chains : basic::options::OptionKeys::pb_potential
chat : basic::options
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::jd2
checkpoint_interval : basic::options::OptionKeys::run
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_min : basic::options::OptionKeys::enzdes
chi_move : basic::options::OptionKeys::relax
childlist : basic::options::OptionKeys::evolution
chilist : basic::options::OptionKeys::willmatch
chirmsd : basic::options::OptionKeys::evaluation
chname : basic::options::OptionKeys::out
choose_random : basic::options::OptionKeys::stepwise
chrisk : basic::options::OptionKeys::chrisk
chtimestamp : basic::options::OptionKeys::out
chunk : basic::options::OptionKeys::chunk
chunks : basic::options::OptionKeys::nonlocal
cin : utility::io::ic
clash_cutoff : basic::options::OptionKeys::pepspec
clash_dis : basic::options::OptionKeys::crossmatch , basic::options::OptionKeys::sicdock , basic::options::OptionKeys::willmatch
classic : basic::options::OptionKeys::relax
clean : basic::options::OptionKeys::run
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
close_chbrk : basic::options::OptionKeys::abinitio
close_enough : basic::options::OptionKeys::motifs
close_loops : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::rigid
close_loops_by_idealizing : basic::options::OptionKeys::abinitio
cluster : basic::options::OptionKeys::cluster , basic::options::OptionKeys::hotspot
cluster_by_all_atom_rmsd : basic::options::OptionKeys::stepwise::protein
cluster_min_volume : basic::options::OptionKeys::packstat
cluster_on_entire_pose : basic::options::OptionKeys::remodel
cluster_radius : basic::options::OptionKeys::remodel
cm : basic::options::OptionKeys::cm
cmiles : basic::options::OptionKeys::cmiles
cognate_partners : basic::options::OptionKeys::pH
cognate_pdb : basic::options::OptionKeys::pH
collect_clustered_top : basic::options::OptionKeys::remodel
colonyE : basic::options::OptionKeys::hotspot
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
compare_native : basic::options::OptionKeys::enzdes
completion_notify_frequency : basic::options::OptionKeys::archive
component_weights : basic::options::OptionKeys::optE
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
conservative_h3_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_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_max : basic::options::OptionKeys::motifs
constraint_skip_rate : basic::options::OptionKeys::fold_cst
constraint_weight : basic::options::OptionKeys::ddg
constraints : basic::options::OptionKeys::constraints , basic::options::OptionKeys::evaluation
constraints_column : basic::options::OptionKeys::evaluation
constraints_NtoC : basic::options::OptionKeys::flxbb
constraints_sheet : basic::options::OptionKeys::flxbb
constraints_sheet_include_cacb_pseudotorsion : basic::options::OptionKeys::flxbb
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
convergence_check_frequency : basic::options::OptionKeys::mc
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
core_cutoff : basic::options::OptionKeys::remodel
correct : basic::options::OptionKeys::corrections
correct_NH_length : basic::options::OptionKeys::rdc
corrected_geo : basic::options::OptionKeys::rna
corrections : basic::options::OptionKeys::corrections
cout : utility::io::oc
cp : basic::options::OptionKeys::cp
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
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
cst : basic::options::OptionKeys::templates::cst
cst_design : basic::options::OptionKeys::enzdes
cst_dock : basic::options::OptionKeys::enzdes
cst_fa_file : basic::options::OptionKeys::constraints
cst_fa_weight : basic::options::OptionKeys::constraints
cst_file : basic::options::OptionKeys::constraints
cst_min : basic::options::OptionKeys::enzdes
cst_opt : basic::options::OptionKeys::enzdes
cst_pdb : basic::options::OptionKeys::RBSegmentRelax
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
cst_width : basic::options::OptionKeys::RBSegmentRelax
cst_wt : basic::options::OptionKeys::RBSegmentRelax
cstfile : basic::options::OptionKeys::enzdes , basic::options::OptionKeys::remodel
cstfilter : basic::options::OptionKeys::remodel
cter_insert : basic::options::OptionKeys::antibody
cterm_seq : basic::options::OptionKeys::assembly
Ctermini : basic::options::OptionKeys::in
CubeSyms : basic::sampling::orientations
cull_with_native : basic::options::OptionKeys::constraints
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
cutoff : basic::options::OptionKeys::cp
cutoutdomain : basic::options::OptionKeys::cutoutdomain
cutpoint_closed : basic::options::OptionKeys::full_model
cutpoint_open : basic::options::OptionKeys::full_model
cycle_ratio : basic::options::OptionKeys::relax
cycles : basic::options::OptionKeys::stepwise::monte_carlo
cycles_inner : basic::options::OptionKeys::run
cycles_outer : basic::options::OptionKeys::run
cyclic_peptide : basic::options::OptionKeys::remodel::RemodelLoopMover
cys_prob : basic::options::OptionKeys::blivens::disulfide_scorer