- c -

• c2_linker_dist() : willmatch
• c2_symm_increment() : willmatch
• C_root() : FloppyTail
• CA() : PhiPsi
• ca_cb_clash_weight() : mh::score
• ca_csts_dev() : fold_from_loops
• Ca_Irms() : evaluation
• ca_mask() : edensity
• ca_ratio() : loodo
• ca_rmsd_cutoff() : fold_from_loops
• calc_binding_energy() : demo::D090_Ala_scan
• calc_pka() : pH::calc_pka
• calc_quadratic() : basic
• calc_rms() : numeric::model_quality
• calc_rms_fast() : numeric::model_quality
• calc_rms_res() : full_model
• calc_rot_boltz() : matdes::mutalyze
• calc_sasa() : pepspec
• calcCAcentroid() : loadPDB
• calcenergy() : pb_potential
• calculate_source_modification_date() : BuildBindings
• callback_structure_name() : binder
• cam_shifts() : evaluation
• camelid() : antibody
• camelid_constraints() : antibody
• canonical_sampling() : canonical_sampling
• cap() : loodo
• cap_e_potential() : fingerprint
• caphit_rt_file() : loodo
• carbohydrates() : carbohydrates
• cart_min() : stepwise::protein
• cartesian() : relax
• CASE_SENSITIVE() : platform::file
• casp() : casp
• cavity_burial_probe_radius() : packstat
• cb_clash_distance() : carbohydrates::clash_check
• cb_sasa_thresh() : willmatch
• cbeta() : remodel
• ccd() : loops::ccd
• ccd_angle() : numeric
• ccd_close() : stepwise::protein
• ccd_closure() : loops
• cdr_definition() : antibody
• cdr_instructions() : antibody::design
• cen_minimize() : remodel
• cen_patch() : loops
• cen_sfxn() : remodel
• cen_weights() : FloppyTail , loops
• cen_wts() : pepspec
• cenpack() : remodel
• cenrot() : corrections::score
• cenrot_cutoff() : packing
• center() : mp::setup , numeric , ObjexxFCL
• center_at_interface() : docking
• center_at_origin() : loadPDB
• center_delta() : mp
• center_mag() : membrane
• center_max_delta() : membrane
• center_of_mass() : numeric
• center_search() : membrane
• center_search_cycles() : mp
• center_start() : mp
• centered() : ObjexxFCL
• centerG_P() : app::surface_docking::surf_param
• centerG_S() : app::surface_docking::surf_param
• central_relax_pdb_num() : pocket_grid
• centroid() : in::file , relax::centroid
• centroid_all_val() : smhybrid
• centroid_density_mass() : edensity , score::fiber_diffraction
• centroid_distance_scale_factor() : frags::contacts
• centroid_input() : in::file
• centroid_loop_mover() : ufv
• centroid_mode() : relax
• centroid_only() : lh
• centroid_output() : stepwise::protein
• centroid_refine() : antibody
• centroid_rot() : optE
• centroid_rot_min() : optE
• centroid_score_diff_cut() : stepwise::protein
• centroid_screen() : stepwise::protein , stepwise::rna
• centroid_sfx() : ufv
• centroid_sfx_patch() : ufv
• centroid_weights() : stepwise::protein
• cg_res_type() : pepspec
• ch_o_bond_potential() : corrections::score
• chain() : run
• chain_break_tol() : loops
• chain_connection() : rna::farna
• chain_from_iterables() : arls_impl
• chain_normal_angle_max() : mp
• chainbreak_bias() : rigid
• chainbreak_max() : fast_loops
• chainbreak_max_accept() : loops
• chainbreak_weight() : AnchoredDesign , relax
• chainbreak_weight_stage1() : jumps
• chainbreak_weight_stage2() : jumps
• chainbreak_weight_stage3() : jumps
• chainbreak_weight_stage4() : jumps
• chainbreaks() : smhybrid
• chainParams() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• chains() : intf
• chains_to_cyclize() : cyclization
• chainTORS() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• chainXYZ() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• change_lig() : enzdes
• change_monolith_library_paths() : toolbox::adjust_library_path
• change_movemap() : templates
• change_namespace_library_paths() : toolbox::adjust_library_path
• CHAR() : ObjexxFCL::Fortran
• char_equali() : ObjexxFCL , utility::file
• char_of() : ObjexxFCL
• charged_chains() : pb_potential
• chat() : basic::options
• check() : fmt::internal
• check_and_print_pdb() : clean_pdb_keep_ligand
• check_cast() : basic
• check_cdr_chainbreaks() : antibody
• check_cdr_pep_bond_geom() : antibody
• check_chains() : carbohydrates::clash_check
• check_rama_scores() : loops::ccd
• check_scored_centroid() : remodel
• check_statement_sanity() : basic::database
• checkpoint() : dna::design , enzdes , fold_from_loops , in::file , ms::checkpoint , remodel , run
• checkpoint_file() : cyclic_peptide , jd2
• checkpoint_interval() : run
• checkpoint_job_identifier() : cyclic_peptide
• chemical() : chemical , corrections::chemical , mistakes::chemical
• chemical_shifts() : evaluation
• chemically_conjugated_docking() : chemically_conjugated_docking
• chi1_increment() : willmatch
• chi2_increment() : willmatch
• chi_iterations() : score::fiber_diffraction
• chi_min() : enzdes
• chi_move() : relax
• childlist() : evolution
• chilist() : willmatch
• chirmsd() : evaluation
• chname() : out
• choose_random() : stepwise
• chtimestamp() : out
• chunk() : chunk
• chunks() : nonlocal
• citation() : app::pyrosetta_toolkit::modules::help
• clamp() : numeric
• CLANG_XML() : tools::CppParser
• clash_check() : carbohydrates::clash_check
• clash_cutoff() : pepspec
• clash_dis() : crossmatch , sicdock , willmatch
• clash_distance_cutoff() : gen_pharmacophore
• class_from_full_path() : exclude
• class_name() : binder
• class_of() : exclude
• class_qualified_name() : binder
• classic() : relax
• clean_whitespace() : app::pyrosetta_toolkit::modules::tools::output
• cleanATOM() : pyrosetta::toolbox , pyrosetta::toolbox::cleaning , toolbox , toolbox::cleaning
• cleanCRYS() : pyrosetta::toolbox , pyrosetta::toolbox::cleaning , toolbox , toolbox::cleaning
• clear_bprots() : motifs
• clear_csts() : fold_from_loops
• clear_pose_cache() : abinitio
• clearLists() : app::pyrosetta_toolkit::window_modules::protocol_builder::ProtocolBuilder
• clock_factor() : basic
• clone_atom_types() : chemical
• close_chbrk() : abinitio
• close_enough() : motifs
• close_loops() : abinitio , rigid , rna::farna
• close_loops_after_each_move() : rna::farna
• close_loops_by_idealizing() : abinitio
• closest_point_on_line() : numeric
• cluster() : cluster , hotspot
• cluster_by_all_atom_rmsd() : stepwise::protein
• cluster_csts_stats_cutoff() : antibody
• cluster_min_volume() : packstat
• cluster_on_entire_pose() : remodel
• cluster_radius() : remodel
• cm() : cm
• cmiles() : cmiles
• cn_symmetry() : score::fiber_diffraction
• code_from_6bit() : utility
• code_to_6bit() : utility
• cognate_partners() : pH
• cognate_pdb() : pH
• colonyE() : hotspot
• coloring_demo() : PyMOL_demo
• com_in_grid() : loodo
• COM_sd() : remodel
• COM_tolerance() : remodel
• COMAS() : numeric::model_quality
• combine() : constraints
• combine_exclude_region() : constraints
• combine_helical_silent_file() : stepwise::rna
• combine_identical_chains() : loadPDB
• combine_long_loop_mode() : stepwise::rna
• combine_names() : utility::file
• combine_rate() : loops
• combine_statistics() : evaluation
• combined_constraints() : evaluation
• combined_constraints_column() : evaluation
• comma_seperated_string_to_xyz() : numeric
• comparable() : ObjexxFCL , utility::keys
• compare_hbonds() : pyrosetta::toolbox::mutants , toolbox::mutants
• compare_mutants__() : pyrosetta::toolbox::mutants , toolbox::mutants
• compare_native() : enzdes
• compare_sequences() : pyrosetta::toolbox::mutants , toolbox::mutants
• compare_times() : compare_times
• completion_notify_frequency() : archive
• component_weights() : optE
• compose() : yaml
• compose_all() : yaml
• compress() : ObjexxFCL
• compute_ddG() : mp_ddG , predict_ddG
• compute_mg_sol_for_hydrogens() : score
• compute_plane_positions() : PyMOLPyRosettaServer
• compute_total_dist_cst() : constraints
• conc() : score
• concat_stringlist() : utility::tag
• cond_exit() : utility
• condenseReslist() : loadPDB
• condor() : run
• config() : frags::scoring , templates
• connect_info_cutoff() : inout
• connect_points() : PyMOLPyRosettaServer
• connection_scheme() : ufv::insert
• conrot() : canonical_sampling::probabilities
• cons_design_data_source() : task_operations
• conservative_framework_design() : antibody::design
• consolidate_matches() : match
• constant_logic_taskops_file() : optE
• constant_seed() : run
• constrain_cter() : antibody
• constrain_P() : rna::farna::erraser
• constrain_relax_segments() : relax
• constrain_relax_to_native_coords() : relax
• constrain_relax_to_start_coords() : relax
• constrain_rigid_segments() : loops
• constrain_vlvh_qq() : antibody
• constrain_weights() : optE
• constraint_skip_rate() : fold_cst
• constraint_weight() : ddg
• constraints() : constraints , evaluation
• constraints_column() : evaluation
• constraints_from_link_records() : in
• constraints_NtoC() : flxbb
• constraints_sheet() : flxbb
• constraints_sheet_include_cacb_pseudotorsion() : flxbb
• construct_kd_tree() : numeric::kdtree
• contact_cutoffE() : pose_metrics
• contact_dis() : sicdock
• contact_dist() : matdes::design
• contact_map() : evaluation
• contact_score() : jumps
• ContactList() : PlotSurfaceContactMap
• ContactMap() : ContactMap
• contactMap() : contactMap
• contacts() : frags::contacts
• context_round() : optE::rescore
• convergence_check_frequency() : mc
• convert() : fmt::internal
• convert_array_to_str() : mp_ddG , predict_ddG
• convert_PDBLIST_to_sqlite3db() : app::pyrosetta_toolkit::modules::tools::output
• convert_to_loadedPDB() : loadPDB
• coord_angle() : coordlib
• coord_constrain_sidechains() : relax
• coord_cst() : loops
• coord_cst_all_atom() : loopfcst
• coord_cst_stdev() : relax
• coord_cst_weight() : loopfcst
• coord_cst_weight_array() : loopfcst
• coord_cst_width() : relax
• coorderr() : mh::filter
• coordinates() : PDBInfo , PhiPsi
• copy_header_directory() : BuildPackagedBindings
• copy_supplemental_files() : build
• copy_tree_contents() : BuildPackagedBindings
• copysign() : utility
• core_cutoff() : remodel
• coreAA() : remodel
• corr_int() : loadPDB
• corrcoef() : numeric::statistics
• corrcoef_with_provided_mean_and_std_dev() : numeric::statistics
• correct() : corrections
• correct_NH_length() : rdc
• corrected_geo() : rna
• corrections() : corrections
• cos_of() : numeric
• cosbeta_increment() : sample_around
• COSFXN() : numeric::crick_equations
• cot() : numeric
• count_digits() : fmt::internal
• count_sc_hbonds() : cyclic_peptide
• cov() : numeric::statistics
• cov_with_provided_mean() : numeric::statistics
• coverage_pow() : mh::score
• cp() : cp
• cpu_frac() : boinc
• cpu_run_time() : boinc
• cpu_run_timeout() : boinc
• create_blank_file() : utility::file
• create_db() : lh
• create_directory() : utility::file
• create_directory_recursive() : utility::file
• create_extra_output() : apps::public1::scenarios::chemically_conjugated_docking
• create_from_secondary_structure() : DenovoProteinDesign
• create_from_template_pdb() : DenovoProteinDesign
• create_package() : build
• create_temp_filename() : utility::file
• createdb_rms_cutoff() : lh
• createRG() : numeric::random
• createSeqFile() : app::pyrosetta_toolkit::modules::tools::output
• cross() : coordlib , numeric , numeric::kinematic_closure , numeric::kinematic_closure::radians , ObjexxFCL
• cross_product() : app::surface_docking::surf_param , Equations , numeric , ObjexxFCL , PhiPsi
• crossmatch() : crossmatch
• cryoem_scatterers() : edensity
• cryst() : cryst
• crystal_refine() : cryst
• csa() : csa , in::file , stepwise::monte_carlo::csa
• csa_bank_size() : stepwise::monte_carlo::csa
• csa_output_rounds() : stepwise::monte_carlo::csa
• csa_rmsd() : stepwise::monte_carlo::csa
• csc() : numeric
• cst() : templates::cst
• cst_design() : enzdes
• cst_dock() : enzdes
• cst_fa_file() : constraints
• cst_fa_only() : remodel
• cst_fa_weight() : constraints
• cst_file() : constraints
• cst_gap() : rna::farna
• cst_min() : enzdes
• cst_opt() : enzdes
• cst_predock() : enzdes
• cst_seqwidth() : RBSegmentRelax
• cst_sub_files() : smhybrid
• cst_weight() : constraints
• cst_weight_coord() : cm::sanitize
• cst_weight_pair() : cm::sanitize
• cstfile() : enzdes , remodel
• cstfilter() : remodel
• cter_insert() : antibody
• Ctermini() : in
• cube() : numeric , ObjexxFCL
• cull_with_native() : constraints
• cumulative() : numeric
• custom_atom_pair() : score
• custom_ff() : score::saxs
• cut1() : enzdes
• cut2() : enzdes
• cut3() : enzdes
• cut4() : enzdes
• cutoff() : cp
• cutoutdomain() : cutoutdomain
• cutpoint_closed() : full_model
• cutpoint_open() : full_model
• cwd() : utility::file
• cycle_ratio() : relax
• cycles() : magnesium::montecarlo , relax::range , rna::farna , stepwise::monte_carlo
• cycles_inner() : run
• cycles_outer() : run
• cyclic_peptide() : abinitio , cyclic_peptide , relax , remodel::RemodelLoopMover
• cyclic_permutations() : cyclic_peptide
• cyclization() : cyclization
• cys_prob() : blivens::disulfide_scorer