Here is a list of all namespace members with links to the namespace documentation for each member:

- c -

• c2_linker_dist : basic::options::OptionKeys::willmatch , willmatch
• c2_symm_increment : basic::options::OptionKeys::willmatch , willmatch
• C_root : basic::options::OptionKeys::FloppyTail , FloppyTail
• ca_csts_dev : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• CA_DME_EVALUATION : basic
• 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_RMSD_EVALUATION : basic
• CacheableDataAP : basic::datacache
• CacheableDataCAP : basic::datacache
• CacheableDataCOP : basic::datacache
• CacheableDataOP : basic::datacache
• CacheableStringAP : basic::datacache
• CacheableStringCAP : basic::datacache
• CacheableStringCOP : basic::datacache
• CacheableStringFloatMapAP : basic::datacache
• CacheableStringFloatMapCAP : basic::datacache
• CacheableStringFloatMapCOP : basic::datacache
• CacheableStringFloatMapOP : basic::datacache
• CacheableStringMapAP : basic::datacache
• CacheableStringMapCAP : basic::datacache
• CacheableStringMapCOP : basic::datacache
• CacheableStringMapOP : basic::datacache
• CacheableStringOP : basic::datacache
• calc_pka : basic::options::OptionKeys::pH::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 : basic::options::OptionKeys::pepspec , pepspec
• calcenergy : basic::options::OptionKeys::pb_potential , pb_potential
• CalculatorOP : numeric
• calls : basic
• 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
• CANONICALMOVER_WRITE_TO_FILE : basic
• carbohydrates : basic::options::OptionKeys::carbohydrates
• cart_min : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• cartesian : basic::options::OptionKeys::relax , relax
• CASE_SENSITIVE() : platform::file
• casp : basic::options::OptionKeys::casp , casp
• cavity_burial_probe_radius : basic::options::OptionKeys::packstat , packstat
• cb_sasa_thresh : basic::options::OptionKeys::willmatch , willmatch
• cbeta : basic::options::OptionKeys::remodel , remodel
• ccd : basic::options::OptionKeys::loops::ccd , loops::ccd
• ccd_angle() : numeric
• CCD_CLOSE : basic
• ccd_close : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• ccd_closure : basic::options::OptionKeys::loops , loops
• cdr_definition() : antibody , basic::options::OptionKeys::antibody
• cen_minimize : basic::options::OptionKeys::remodel , remodel
• cen_patch : basic::options::OptionKeys::loops , loops
• cen_sfxn : basic::options::OptionKeys::remodel , remodel
• cen_weights : basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys::loops , FloppyTail , loops
• cen_wts : basic::options::OptionKeys::pepspec , pepspec
• cenpack : basic::options::OptionKeys::remodel , remodel
• cenrot : basic::options::OptionKeys::corrections::score , corrections::score
• cenrot_cutoff : basic::options::OptionKeys::packing , packing
• center : basic::options::OptionKeys::membrane_new::setup , membrane_new::setup , numeric
• center_at_interface : basic::options::OptionKeys::docking , docking
• center_atoms_at_origin() : numeric::model_quality
• center_delta : basic::options::OptionKeys::membrane_new , membrane_new
• center_mag : basic::options::OptionKeys::membrane , membrane
• center_max_delta : basic::options::OptionKeys::membrane , membrane
• center_of_mass() : numeric
• center_of_mass_binned : numeric::geometry::hashing
• center_search : basic::options::OptionKeys::membrane , membrane
• center_search_cycles : basic::options::OptionKeys::membrane_new , membrane_new
• center_start : basic::options::OptionKeys::membrane_new , membrane_new
• central_relax_pdb_num : basic::options::OptionKeys::pocket_grid , pocket_grid
• centroid : basic::options::OptionKeys::in::file , basic::options::OptionKeys::relax::centroid , in::file , relax::centroid
• centroid_all_val : basic::options::OptionKeys::smhybrid , 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 : basic::options::OptionKeys::ufv , ufv
• centroid_mode : basic::options::OptionKeys::relax , relax
• centroid_only : basic::options::OptionKeys::lh , lh
• centroid_output : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• centroid_refine() : antibody , basic::options::OptionKeys::antibody
• centroid_score_diff_cut : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• centroid_screen : basic::options::OptionKeys::stepwise::protein , basic::options::OptionKeys::stepwise::rna , stepwise::protein , stepwise::rna
• centroid_sfx : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::ufv , ufv
• centroid_sfx_patch : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::ufv , ufv
• centroid_weights : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• cerr : utility::io::oc
• cg_res_type : basic::options::OptionKeys::pepspec , pepspec
• ch_o_bond_potential : basic::options::OptionKeys::corrections::score , corrections::score
• chain : basic::options::OptionKeys::run , run
• chain_break_tol : basic::options::OptionKeys::loops , loops
• chain_normal_angle_max : basic::options::OptionKeys::membrane_new , membrane_new
• chainbreak_bias : basic::options::OptionKeys::rigid , 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 , basic::options::OptionKeys::relax , 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 : basic::options::OptionKeys::smhybrid , smhybrid
• chainParams() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• chains_to_cyclize : basic::options::OptionKeys::cyclization , cyclization
• 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 : basic::options::OptionKeys::templates , templates
• char_equali() : utility::file
• charged_chains : basic::options::OptionKeys::pb_potential , pb_potential
• chat : basic::options
• check_cast() : basic
• check_cdr_chainbreaks() : antibody , basic::options::OptionKeys::antibody
• check_cdr_pep_bond_geom() : antibody , basic::options::OptionKeys::antibody
• CHECK_COMM_SIZE : basic
• check_rama_scores : basic::options::OptionKeys::loops::ccd , loops::ccd
• check_scored_centroid : basic::options::OptionKeys::remodel , 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 , basic::options::OptionKeys::remodel , basic::options::OptionKeys::run , dna::design , enzdes , fold_from_loops , in::file , ms::checkpoint , remodel , run
• checkpoint_file : basic::options::OptionKeys::jd2 , jd2
• checkpoint_interval : basic::options::OptionKeys::run , run
• chemical : basic::options::OptionKeys::chemical , basic::options::OptionKeys::corrections::chemical , basic::options::OptionKeys::mistakes::chemical , chemical , corrections::chemical , mistakes::chemical
• CHEMICAL_MAKE_POSE : basic
• chemical_shifts : basic::options::OptionKeys::evaluation , evaluation
• chemically_conjugated_docking : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• chi1_increment : basic::options::OptionKeys::willmatch , willmatch
• chi2_increment : basic::options::OptionKeys::willmatch , willmatch
• chi_min : basic::options::OptionKeys::enzdes , enzdes
• chi_move : basic::options::OptionKeys::relax , relax
• childlist : basic::options::OptionKeys::evolution , evolution
• chilist : basic::options::OptionKeys::willmatch , willmatch
• chirmsd : basic::options::OptionKeys::evaluation , evaluation
• chname : basic::options::OptionKeys::out , out
• choose_random : basic::options::OptionKeys::stepwise , stepwise
• chrisk : basic::options::OptionKeys::chrisk
• chtimestamp : basic::options::OptionKeys::out , out
• chunk : basic::options::OptionKeys::chunk , chunk
• chunks : basic::options::OptionKeys::nonlocal , nonlocal
• cin : utility::io::ic
• clamp() : numeric
• clash_cutoff : basic::options::OptionKeys::pepspec , pepspec
• clash_dis : basic::options::OptionKeys::crossmatch , basic::options::OptionKeys::sicdock , basic::options::OptionKeys::willmatch , crossmatch , sicdock , willmatch
• classic : basic::options::OptionKeys::relax , relax
• 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
• clog : utility::io::oc
• close_chbrk() : abinitio , basic::options::OptionKeys::abinitio
• close_enough : basic::options::OptionKeys::motifs , motifs , numeric::model_quality
• close_loops() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::rigid , 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 : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• cluster_min_volume : basic::options::OptionKeys::packstat , packstat
• cluster_on_entire_pose : basic::options::OptionKeys::remodel , remodel
• cluster_radius : basic::options::OptionKeys::remodel , remodel
• ClusteringTreeNodeOP : numeric
• cm : basic::options::OptionKeys::cm , cm
• cmiles : basic::options::OptionKeys::cmiles , cmiles
• code_from_6bit() : utility
• code_to_6bit() : utility
• cognate_partners : basic::options::OptionKeys::pH , pH
• cognate_pdb : basic::options::OptionKeys::pH , pH
• colonyE : basic::options::OptionKeys::hotspot , hotspot
• ColumnCOP : basic::database::schema_generator
• ColumnOP : basic::database::schema_generator
• Columns : basic::database::schema_generator
• COM_sd : basic::options::OptionKeys::remodel , remodel
• COM_tolerance : basic::options::OptionKeys::remodel , remodel
• COMAS() : numeric::model_quality
• combine : basic::options::OptionKeys::constraints , constraints
• combine_exclude_region : basic::options::OptionKeys::constraints , constraints
• combine_helical_silent_file : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• combine_long_loop_mode : basic::options::OptionKeys::stepwise::rna , 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
• COMM_REDUCE_SIZE : basic
• COMMA : numeric::expression_parser
• 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
• CompoundInterpolatorCOP : numeric::interpolation::spline
• CompoundInterpolatorOP : numeric::interpolation::spline
• compute_total_dist_cst : basic::options::OptionKeys::constraints , constraints
• conc : basic::options::OptionKeys::score , score
• cond_exit() : utility
• condor : basic::options::OptionKeys::run , run
• config : basic::options::OptionKeys::frags::scoring , basic::options::OptionKeys::templates , frags::scoring , templates
• Config : utility::json_spirit
• CONFORMATION_COPY : basic
• CONFORMATION_DETECT_DISULF : basic
• CONFORMATION_FIX_DISULF : basic
• connect_info_cutoff : basic::options::OptionKeys::inout , inout
• connection_scheme : basic::options::OptionKeys::ufv::insert , 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_iterator : basic::options::OptionKeys , utility::options::OptionKeys
• const_pointer_cast() : utility::pointer
• constant_logic_taskops_file : basic::options::OptionKeys::optE , optE
• constant_seed : basic::options::OptionKeys::run , run
• ConstIterator : basic::options::OptionKeys , utility::options::OptionKeys
• constrain_cter() : antibody , basic::options::OptionKeys::antibody
• constrain_relax_segments : basic::options::OptionKeys::relax , relax
• constrain_relax_to_native_coords : basic::options::OptionKeys::relax , relax
• constrain_relax_to_start_coords : basic::options::OptionKeys::relax , 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_SCORE : basic
• CONSTRAINT_SET_COPY : basic
• constraint_skip_rate : basic::options::OptionKeys::fold_cst , fold_cst
• constraint_weight : basic::options::OptionKeys::ddg , ddg
• ConstraintCOP : basic::database::schema_generator
• ConstraintOP : basic::database::schema_generator
• 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_DISTANCE_MATRIX : basic
• construct_kd_tree() : numeric::kdtree
• contact_cutoffE : basic::options::OptionKeys::pose_metrics , pose_metrics
• contact_dis : basic::options::OptionKeys::sicdock , 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 : basic::options::OptionKeys::relax , relax
• coord_cst : basic::options::OptionKeys::loops , loops
• coord_cst_all_atom() : basic::options::OptionKeys::loopfcst , loopfcst
• coord_cst_stdev : basic::options::OptionKeys::relax , relax
• coord_cst_weight : basic::options::OptionKeys::loopfcst , loopfcst
• coord_cst_weight_array() : basic::options::OptionKeys::loopfcst , loopfcst
• coord_cst_width : basic::options::OptionKeys::relax , relax
• coorderr : basic::options::OptionKeys::mh::filter , mh::filter
• Coordinate : numeric::kinematic_closure
• CoordinateList : numeric::kinematic_closure
• COPY_COORDS : basic
• copysign() : utility
• core_cutoff : basic::options::OptionKeys::remodel , remodel
• corrcoef() : numeric::statistics
• corrcoef_with_provided_mean_and_std_dev() : numeric::statistics
• correct() : basic::options::OptionKeys::corrections , corrections
• correct_NH_length : basic::options::OptionKeys::rdc , rdc
• corrected_geo : basic::options::OptionKeys::rna , rna
• corrections() : basic::options::OptionKeys::corrections , corrections
• cos_of() : numeric
• cot() : numeric
• cout : utility::io::oc
• 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 : basic::options::OptionKeys::templates::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_predock : basic::options::OptionKeys::enzdes , enzdes
• cst_seqwidth : basic::options::OptionKeys::RBSegmentRelax , RBSegmentRelax
• cst_sub_files : basic::options::OptionKeys::smhybrid , 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
• cstfile : basic::options::OptionKeys::enzdes , enzdes
• cstfilter : basic::options::OptionKeys::remodel , remodel
• cter_insert() : antibody , basic::options::OptionKeys::antibody
• Ctermini : basic::options::OptionKeys::in , in
• cube() : numeric
• CubeSyms : basic::sampling::orientations
• cull_with_native() : basic::options::OptionKeys::constraints , constraints
• cumulative() : numeric
• custom_atom_pair : basic::options::OptionKeys::score , score
• custom_ff : basic::options::OptionKeys::score::saxs , 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 : basic::options::OptionKeys::relax , relax
• cycles : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• cycles_inner : basic::options::OptionKeys::run , run
• cycles_outer : basic::options::OptionKeys::run , run
• cyclic_peptide : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• cyclization() : basic::options::OptionKeys::cyclization , cyclization
• cys_prob() : basic::options::OptionKeys::blivens::disulfide_scorer , blivens::disulfide_scorer