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_cstring : ObjexxFCL , ObjexxFCL::format
• c_cyd_seqpos : basic::options::OptionKeys::DisulfideInsertion , DisulfideInsertion
• C_root : basic::options::OptionKeys::FloppyTail , FloppyTail
• ca_cb_clash_weight : basic::options::OptionKeys::mh::score , mh::score
• 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_MODEL : clean_pdb_keep_ligand
• ca_ratio : basic::options::OptionKeys::loodo , loodo
• ca_rmsd_cutoff : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• CA_RMSD_EVALUATION : basic
• CA_xyz : test::Workshop2test
• 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
• CacheableStringIntegerMapAP : basic::datacache
• CacheableStringIntegerMapCAP : basic::datacache
• CacheableStringIntegerMapCOP : basic::datacache
• CacheableStringIntegerMapOP : basic::datacache
• CacheableStringMapAP : basic::datacache
• CacheableStringMapCAP : basic::datacache
• CacheableStringMapCOP : basic::datacache
• CacheableStringMapOP : basic::datacache
• CacheableStringOP : basic::datacache
• CacheableUint64MathMatrixFloatMapAP : basic::datacache
• CacheableUint64MathMatrixFloatMapCAP : basic::datacache
• CacheableUint64MathMatrixFloatMapCOP : basic::datacache
• CacheableUint64MathMatrixFloatMapOP : basic::datacache
• calc_binding_energy() : demo::D090_Ala_scan
• calc_dihedral() : pyrosetta::toolbox::numpy_utils
• 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
• calc_zscore() : numeric
• calcenergy : basic::options::OptionKeys::pb_potential , pb_potential
• calcium_motif_score_weight : basic::options::OptionKeys::legacy_sewing , legacy_sewing
• calculate_dihedral_distance() : numeric::model_quality
• CalculatorOP : numeric
• call_back_function_body_template : binder
• callback_structure_name() : binder
• calls : basic
• cam_shifts : basic::options::OptionKeys::evaluation , evaluation
• camelid() : antibody , basic::options::OptionKeys::antibody
• camelid_constraints() : antibody , basic::options::OptionKeys::antibody
• canonical_res_char_string() : utility::tag
• canonical_sampling : basic::options::OptionKeys::canonical_sampling , canonical_sampling
• CANONICALMOVER_WRITE_TO_FILE : basic
• cap : basic::options::OptionKeys::loodo , loodo
• cap_e_potential : basic::options::OptionKeys::fingerprint , fingerprint
• caphit_rt_file : basic::options::OptionKeys::loodo , loodo
• carbohydrates : basic::options::OptionKeys::carbohydrates , carbohydrates
• CArray_bool : ObjexxFCL
• CArray_byte : ObjexxFCL
• CArray_char : ObjexxFCL
• CArray_double : ObjexxFCL
• CArray_float : ObjexxFCL
• CArray_Fstring : ObjexxFCL
• CArray_int : ObjexxFCL
• CArray_long : ObjexxFCL
• CArray_longdouble : ObjexxFCL
• CArray_sbyte : ObjexxFCL
• CArray_schar : ObjexxFCL
• CArray_short : ObjexxFCL
• CArray_size : ObjexxFCL
• CArray_size_t : ObjexxFCL
• CArray_string : ObjexxFCL
• CArray_ubyte : ObjexxFCL
• CArray_uchar : ObjexxFCL
• CArray_uint : ObjexxFCL
• CArray_ulong : ObjexxFCL
• CArray_ushort : ObjexxFCL
• CArrayP_bool : ObjexxFCL
• CArrayP_byte : ObjexxFCL
• CArrayP_char : ObjexxFCL
• CArrayP_double : ObjexxFCL
• CArrayP_float : ObjexxFCL
• CArrayP_Fstring : ObjexxFCL
• CArrayP_int : ObjexxFCL
• CArrayP_long : ObjexxFCL
• CArrayP_longdouble : ObjexxFCL
• CArrayP_sbyte : ObjexxFCL
• CArrayP_schar : ObjexxFCL
• CArrayP_short : ObjexxFCL
• CArrayP_size : ObjexxFCL
• CArrayP_size_t : ObjexxFCL
• CArrayP_string : ObjexxFCL
• CArrayP_ubyte : ObjexxFCL
• CArrayP_uchar : ObjexxFCL
• CArrayP_uint : ObjexxFCL
• CArrayP_ulong : ObjexxFCL
• CArrayP_ushort : ObjexxFCL
• cart_min : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• cartesian : basic::options::OptionKeys::ddg , basic::options::OptionKeys::relax , ddg , relax
• cartesian_relax_rounds : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• cartmin : basic::options::OptionKeys::carbohydrates::glycan_sampler , carbohydrates::glycan_sampler
• CASE_SENSITIVE() : platform::file
• casp : basic::options::OptionKeys::casp , casp
• category : pyrosetta::utility::array
• catmull_rom_interpolate() : numeric::interpolation
• catmull_rom_interpolate_basic() : numeric::interpolation
• CatmullRomSplineBoundaryType : numeric::interpolation
• cavity_burial_probe_radius : basic::options::OptionKeys::packstat , packstat
• cb_clash_distance : basic::options::OptionKeys::carbohydrates::clash_check , carbohydrates::clash_check
• cb_sasa_thresh : basic::options::OptionKeys::willmatch , willmatch
• cbeta : basic::options::OptionKeys::remodel , remodel
• ccd : basic::options::OptionKeys::loops::ccd , loops::ccd , test::Workshop8test
• ccd_angle() : numeric
• CCD_CLOSE : basic
• ccd_close : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• ccd_closure : basic::options::OptionKeys::loops , loops
• CD : pyrosetta
• cdr_definition() : antibody , basic::options::OptionKeys::antibody
• cdr_instructions() : antibody::design , basic::options::OptionKeys::antibody::design
• cdr_set_cache_limit() : antibody::design , basic::options::OptionKeys::antibody::design
• cdrs : test::G201_Module_Structure
• 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::mp::setup , mp::setup , numeric , ObjexxFCL
• center_at_interface : basic::options::OptionKeys::docking , docking
• center_delta : basic::options::OptionKeys::mp , mp
• center_jumps_in_single_stranded : basic::options::OptionKeys::rna::denovo , rna::denovo
• 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::mp , mp
• center_start : basic::options::OptionKeys::mp , mp
• centered() : ObjexxFCL
• 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 , basic::options::OptionKeys::score::fiber_diffraction , edensity , score::fiber_diffraction
• 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_rot : basic::options::OptionKeys::optE , optE
• centroid_rot_min : basic::options::OptionKeys::optE , optE
• 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::ufv , ufv
• centroid_sfx_patch : basic::options::OptionKeys::ufv , ufv
• centroid_weights : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• cereal : pyrosetta::distributed::utility::pickle
• 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_connection : basic::options::OptionKeys::rna::denovo , rna::denovo
• chain_cslist_string() : utility::tag
• chain_from_iterables() : arls_impl
• chain_normal_angle_max : basic::options::OptionKeys::mp , mp
• 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
• chainid : clean_pdb_keep_ligand
• chainParams() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• chains : basic::options::OptionKeys::intf , intf
• chains_to_cyclize : basic::options::OptionKeys::cyclization , cyclization
• chains_to_ignore : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering
• 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() : ObjexxFCL::Fortran
• char_equali() : ObjexxFCL , utility::file
• CHAR_FLAG : fmt
• char_of() : ObjexxFCL
• charged_chains : basic::options::OptionKeys::pb_potential , pb_potential
• chat : basic::options
• check_all_PDB_components : basic::options::OptionKeys::in::file , in::file
• check_and_print_pdb() : clean_pdb_keep_ligand
• check_cast() : basic
• check_cdr_chainbreaks() : antibody , basic::options::OptionKeys::antibody
• check_cdr_pep_bond_geom() : antibody , basic::options::OptionKeys::antibody
• check_chains : basic::options::OptionKeys::carbohydrates::clash_check , carbohydrates::clash_check
• CHECK_COMM_SIZE : basic
• check_for_chain_breaks() : apps::pilot::frankdt
• check_motifs() : apps::pilot::frankdt
• check_path_exist() : erraser_util
• check_rama_scores : basic::options::OptionKeys::loops::ccd , loops::ccd
• check_scored_centroid : basic::options::OptionKeys::remodel , remodel
• check_sign() : fmt::internal
• 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::cyclic_peptide , basic::options::OptionKeys::jd2 , cyclic_peptide , jd2
• checkpoint_interval : basic::options::OptionKeys::run , run
• checkpoint_job_identifier : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• checkpointing_frequency : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• 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_iterations : basic::options::OptionKeys::score::fiber_diffraction , score::fiber_diffraction
• chi_list1 : erraser_analysis
• chi_list2 : erraser_analysis
• chi_min : basic::options::OptionKeys::enzdes , enzdes
• chi_move : basic::options::OptionKeys::relax , relax
• chi_stdev : basic::options::OptionKeys::recces::thermal_sampling , recces::thermal_sampling
• childlist : basic::options::OptionKeys::evolution , evolution
• chilist : basic::options::OptionKeys::willmatch , willmatch
• chirmsd : basic::options::OptionKeys::evaluation , evaluation
• chm : test::T100_Basic
• chname : basic::options::OptionKeys::out , out
• choose_random : basic::options::OptionKeys::stepwise , stepwise
• chr_chains_nonrepeated() : utility::tag
• chtimestamp : basic::options::OptionKeys::out , out
• chunk : basic::options::OptionKeys::chunk , chunk
• chunks : basic::options::OptionKeys::nonlocal , nonlocal
• ChunkVector_bool : ObjexxFCL
• ChunkVector_byte : ObjexxFCL
• ChunkVector_char : ObjexxFCL
• ChunkVector_double : ObjexxFCL
• ChunkVector_float : ObjexxFCL
• ChunkVector_Fstring : ObjexxFCL
• ChunkVector_int : ObjexxFCL
• ChunkVector_long : ObjexxFCL
• ChunkVector_longdouble : ObjexxFCL
• ChunkVector_sbyte : ObjexxFCL
• ChunkVector_schar : ObjexxFCL
• ChunkVector_short : ObjexxFCL
• ChunkVector_size : ObjexxFCL
• ChunkVector_size_t : ObjexxFCL
• ChunkVector_string : ObjexxFCL
• ChunkVector_ubyte : ObjexxFCL
• ChunkVector_uchar : ObjexxFCL
• ChunkVector_uint : ObjexxFCL
• ChunkVector_ulong : ObjexxFCL
• ChunkVector_ushort : ObjexxFCL
• cif_extra_data_separate_file : basic::options::OptionKeys::out::file , out::file
• cin : utility::io::ic
• circle : test::Workshop9test
• circle2 : test::Workshop9test
• clamp() : numeric
• clash1 : erraser_analysis
• clash2 : erraser_analysis
• clash_check : basic::options::OptionKeys::carbohydrates::clash_check , carbohydrates::clash_check
• clash_cutoff : basic::options::OptionKeys::pepspec , pepspec
• clash_dis : basic::options::OptionKeys::crossmatch , basic::options::OptionKeys::sicdock , basic::options::OptionKeys::willmatch , crossmatch , sicdock , willmatch
• clash_distance_cutoff : basic::options::OptionKeys::gen_pharmacophore , gen_pharmacophore
• class_name() : binder
• class_qualified_name() : binder
• classic : basic::options::OptionKeys::relax , relax
• clean : basic::options::OptionKeys::cloud , cloud
• cleanATOM() : pyrosetta::toolbox::cleaning
• cleanCRYS() : pyrosetta::toolbox::cleaning
• 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
• clone_atom_types : basic::options::OptionKeys::chemical , chemical
• close_chbrk() : abinitio , basic::options::OptionKeys::abinitio
• close_enough : basic::options::OptionKeys::motifs , motifs
• close_loops() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::rigid , basic::options::OptionKeys::rna::denovo , rigid , rna::denovo
• close_loops_after_each_move : basic::options::OptionKeys::rna::denovo , rna::denovo
• close_loops_by_idealizing() : abinitio , basic::options::OptionKeys::abinitio
• closest_point_on_line() : numeric
• cloud : basic::options::OptionKeys::cloud , cloud
• cluster : basic::options::OptionKeys::cluster , basic::options::OptionKeys::hotspot , cluster , hotspot
• cluster_by : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering
• cluster_by_all_atom_rmsd : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• cluster_csts_stats_cutoff() : antibody , basic::options::OptionKeys::antibody
• cluster_cutoff : basic::options::OptionKeys::corrections::water , corrections::water
• cluster_cyclic_permutations : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering
• cluster_min_volume : basic::options::OptionKeys::packstat , packstat
• cluster_on_entire_pose : basic::options::OptionKeys::remodel , remodel
• cluster_radius : basic::options::OptionKeys::cluster::energy_based_clustering , basic::options::OptionKeys::corrections::water , basic::options::OptionKeys::remodel , cluster::energy_based_clustering , corrections::water , remodel
• ClusteringTreeNodeAP : numeric
• ClusteringTreeNodeOP : numeric
• cm : basic::options::OptionKeys::cm , cm
• cmake_needs_to_be_run() : build
• cmiles : basic::options::OptionKeys::cmiles , cmiles
• cn_symmetry : basic::options::OptionKeys::score::fiber_diffraction , score::fiber_diffraction
• code_from_6bit() : utility
• code_to_6bit() : utility
• cognate_partners : basic::options::OptionKeys::pH , pH
• cognate_pdb : basic::options::OptionKeys::pH , pH
• collect_python_modules() : sphinx-doc-generator
• colonyE : basic::options::OptionKeys::hotspot , hotspot
• Color : fmt
• COLOR_LIB : PyMOL-RosettaServer
• coloring_demo() : PyMOL_demo
• colors : test::T150_PyMOL_Integration
• ColumnCOP : basic::database::schema_generator
• ColumnOP : basic::database::schema_generator
• Columns : basic::database::schema_generator
• com_in_grid : basic::options::OptionKeys::loodo , loodo
• COM_root : basic::options::OptionKeys::FloppyTail , FloppyTail
• 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_pdbs() : combine_pdbs
• 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
• commit : version
• commit_id : version
• comparable() : ObjexxFCL , utility::keys
• compare_native : basic::options::OptionKeys::enzdes , enzdes
• compare_residue_energies_all : local
• compare_residue_energies_mut : local
• compare_segment_to_motif() : apps::pilot::frankdt
• compare_times() : compare_times
• compile_sources() : make_bindings_via_cmake
• completion_notify_frequency() : archive , basic::options::OptionKeys::archive
• component_weights : basic::options::OptionKeys::optE , optE
• CompoundInterpolatorCOP : numeric::interpolation::spline
• CompoundInterpolatorOP : numeric::interpolation::spline
• compress() : ObjexxFCL
• compress_job_results : basic::options::OptionKeys::jd3 , jd3
• compute_angle() : measure_params
• compute_ddG() : mp_ddG
• compute_dist() : measure_params
• compute_mg_sol_for_hydrogens : basic::options::OptionKeys::score , score
• compute_plane_positions() : PyMOL-RosettaServer
• compute_squared_dist() : measure_params
• compute_torsion() : measure_params
• compute_total_dist_cst : basic::options::OptionKeys::constraints , constraints
• conc : basic::options::OptionKeys::score , score
• concat_stringlist() : utility::tag
• 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
• connect_points() : PyMOL-RosettaServer
• connection_scheme : basic::options::OptionKeys::ufv::insert , ufv::insert
• conrot : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• cons_design_data_source : basic::options::OptionKeys::task_operations , task_operations
• conservative_framework_design() : antibody::design , basic::options::OptionKeys::antibody::design
• consolidate_matches : basic::options::OptionKeys::match , match
• const_access_Real_MathNTensor() : numeric
• const_check() : fmt::internal
• constant_logic_taskops_file : basic::options::OptionKeys::optE , optE
• constant_seed : basic::options::OptionKeys::run , run
• ConstDataMapCOP : basic::datacache
• ConstDataMapOP : basic::datacache
• constrain_cter() : antibody , basic::options::OptionKeys::antibody
• constrain_P : basic::options::OptionKeys::rna::erraser , rna::erraser
• 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 , basic::options::OptionKeys::DisulfideInsertion , ddg , DisulfideInsertion , local
• 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_from_link_records : basic::options::OptionKeys::in , in
• 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
• constructor_template : binder
• constructor_with_trampoline_template : binder
• 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
• contains() : utility
• context_round : basic::options::OptionKeys::optE::rescore , optE::rescore
• continue_until_none_missing : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• convergence_check_frequency : basic::options::OptionKeys::mc , mc
• convert() : fmt::internal
• convert_array_to_str() : mp_ddG
• convert_protein_CEN : basic::options::OptionKeys::rna::denovo , rna::denovo
• 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
• coordinate_array_broadcast_rmsd() : numeric::alignment , pyrosetta::numeric::alignment::rmsd_calc
• coordinate_array_broadcast_rmsd< float >() : numeric::alignment
• coordinate_array_broadcast_rmsd< numeric::Real >() : numeric::alignment
• coordinate_array_rmsd() : numeric::alignment , pyrosetta::numeric::alignment::rmsd_calc
• coordinate_array_rmsd< float >() : numeric::alignment
• coordinate_array_rmsd< numeric::Real >() : numeric::alignment
• coordinate_array_superimpose() : numeric::alignment
• coordinate_array_superimpose< float >() : numeric::alignment
• coordinate_array_superimpose< numeric::Real >() : numeric::alignment
• coordinate_array_to_atoms() : pyrosetta::utility::array
• coordinate_array_unaligned_broadcast_rmsd() : pyrosetta::numeric::alignment::rmsd_calc
• CoordinateList : numeric::kinematic_closure
• copy() : erraser_util
• COPY_COORDS : basic
• copy_set_to_vector() : apps::pilot::frankdt
• copyright : conf
• copysign() : utility
• core_cutoff : basic::options::OptionKeys::remodel , remodel
• coreAA : 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
• correct_sign : basic::options::OptionKeys::nmr::rdc , nmr::rdc
• corrected_geo : basic::options::OptionKeys::rna , rna
• corrections : basic::options::OptionKeys::corrections , corrections
• cos_of() : numeric
• cosbeta_increment : basic::options::OptionKeys::sample_around , sample_around
• COSFXN() : numeric::crick_equations
• cot() : numeric
• count : clean_pdb_keep_ligand
• count_digits() : fmt::internal
• count_pair_hybrid : basic::options::OptionKeys::score , score
• count_sc_hbonds : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• counter : demo::D060_Folding , demo::D100_Docking , demo::D110_DNA_interface , demo::D120_Ligand_interface
• coupled_moves : basic::options::OptionKeys::coupled_moves , coupled_moves
• cout : utility::io::oc
• cov() : numeric::statistics
• cov_with_provided_mean() : numeric::statistics
• covalent_labeling_fa_input : basic::options::OptionKeys::score , score
• covalent_labeling_input : basic::options::OptionKeys::score , score
• coverage_pow : basic::options::OptionKeys::mh::score , mh::score
• cp : basic::options::OptionKeys::cp , cp
• cpp_python_operator_map : binder
• cpp_set : test::T040_Types
• cpu_frac : basic::options::OptionKeys::boinc , boinc
• cpu_run_time : basic::options::OptionKeys::boinc , boinc
• cpu_run_timeout : basic::options::OptionKeys::boinc , boinc
• create_blank_file() : utility::file
• create_db : basic::options::OptionKeys::lh , lh
• create_directory() : utility::file
• create_directory_recursive() : utility::file
• create_extra_output() : apps::public1::scenarios::chemically_conjugated_docking
• create_from_secondary_structure : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• create_from_template_pdb : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• create_package() : build
• create_score_function : pyrosetta
• create_temp_filename() : utility::file
• create_wheel() : build
• createdb_rms_cutoff : basic::options::OptionKeys::lh , lh
• createRG() : numeric::random
• cross() : measure_params , numeric , numeric::kinematic_closure , numeric::kinematic_closure::radians , ObjexxFCL
• cross_product() : numeric , ObjexxFCL
• crossmatch : basic::options::OptionKeys::crossmatch , crossmatch
• 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 , basic::options::OptionKeys::stepwise::monte_carlo::csa , csa , in::file , stepwise::monte_carlo::csa
• csa_bank_size : basic::options::OptionKeys::stepwise::monte_carlo::csa , stepwise::monte_carlo::csa
• csa_output_rounds : basic::options::OptionKeys::stepwise::monte_carlo::csa , stepwise::monte_carlo::csa
• csa_rmsd : basic::options::OptionKeys::stepwise::monte_carlo::csa , stepwise::monte_carlo::csa
• csc() : numeric
• CSI_bgBlack() : utility
• CSI_bgBlue() : utility
• CSI_bgCyan() : utility
• CSI_bgDefault() : utility
• CSI_bgGreen() : utility
• CSI_bgMagenta() : utility
• CSI_bgRed() : utility
• CSI_bgWhite() : utility
• CSI_bgYellow() : utility
• CSI_Black() : utility
• CSI_Blue() : utility
• CSI_Bold() : utility
• CSI_Cyan() : utility
• CSI_Default() : utility
• CSI_Enum : utility::CSI
• CSI_Green() : utility
• CSI_Magenta() : utility
• CSI_Nothing() : utility
• CSI_Red() : utility
• CSI_Reset() : utility
• CSI_Underline() : utility
• CSI_White() : utility
• CSI_Yellow() : utility
• cst : basic::options::OptionKeys::templates::cst , templates::cst
• cst_design : basic::options::OptionKeys::enzdes , enzdes
• cst_dist_cutoff : basic::options::OptionKeys::ddg , ddg
• cst_dock : basic::options::OptionKeys::enzdes , enzdes
• cst_fa_file : basic::options::OptionKeys::constraints , constraints
• cst_fa_only : basic::options::OptionKeys::remodel , remodel
• cst_fa_weight : basic::options::OptionKeys::constraints , constraints
• cst_file : basic::options::OptionKeys::cluster::energy_based_clustering , basic::options::OptionKeys::constraints , cluster::energy_based_clustering , constraints , test::G100_Functions_Input
• cst_gap : basic::options::OptionKeys::rna::denovo , rna::denovo
• 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 , basic::options::OptionKeys::remodel , enzdes , remodel
• cstfilter : basic::options::OptionKeys::remodel , remodel
• cstring : ObjexxFCL , ObjexxFCL::format
• CStringRef : fmt
• cter_insert() : antibody , basic::options::OptionKeys::antibody
• Ctermini : basic::options::OptionKeys::in , in
• CTGenSubelementBehavior : utility::tag
• cube() : numeric , ObjexxFCL
• CubeSyms : basic::sampling::orientations
• cubic_polynomial_deriv() : numeric
• cubic_polynomial_from_spline() : numeric
• CubicSplineCOP : numeric::interpolation::spline
• CubicSplineOP : numeric::interpolation::spline
• cull_with_native : basic::options::OptionKeys::constraints , constraints
• cumulative() : numeric
• current_chunk : rna_decompose
• 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
• cut_at_rna_chainbreak : basic::options::OptionKeys::rna , rna
• cutoff : basic::options::OptionKeys::cp , cp
• cutoutdomain : basic::options::OptionKeys::cutoutdomain , cutoutdomain
• cutpoint : loops
• cutpoint_closed : basic::options::OptionKeys::full_model , full_model
• cutpoint_open : basic::options::OptionKeys::full_model , full_model
• cwd() : utility::file
• CYAN : fmt
• Cyan : utility::CSI
• cycle_ratio : basic::options::OptionKeys::relax , 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 , magnesium::montecarlo , relax::range , rna::denovo , stepwise::monte_carlo
• cycles_inner : basic::options::OptionKeys::run , run
• cycles_outer : basic::options::OptionKeys::run , run
• cyclic : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering , peptoid_design
• cyclic_peptide() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::cyclic_peptide , basic::options::OptionKeys::relax , basic::options::OptionKeys::remodel::RemodelLoopMover , cyclic_peptide , relax , remodel::RemodelLoopMover
• cyclic_permutation_offset : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering
• cyclic_permutations : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• cyclic_symmetry : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering
• cyclic_symmetry_mirroring : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering
• cyclic_symmetry_threshold : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering
• cyclization : basic::options::OptionKeys::cyclization , cyclization
• cyclization_type : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• cyclize : basic::options::OptionKeys::full_model , full_model
• cys_prob : basic::options::OptionKeys::blivens::disulfide_scorer , blivens::disulfide_scorer