- c -

• CA_cst_generator() : fold_from_loops.cc
• CA_distance() : disulfides.hh
• ca_to_allatom_main() : ca_to_allatom.cc
• cal_distance() : rms_util.hh
• cal_rmsd() : rms_util.hh
• cal_score() : clash_score.hh
• calc_B_values() : SID_ERMS_prediction.cc
• calc_base_centroid_rmsd() : rb_entropy.cc
• calc_blosum_scores() : james_util.hh
• calc_burial() : outputLayerDesignBurial.cc , outputSasa.cc
• calc_c3_rmsd() : hubabinitio.cc , hubfragdesign.cc
• calc_contacts() : contact_map_from_homologs.cc
• calc_ddg() : score_ddgs.cc
• calc_dgaps() : james_util.hh
• calc_dihedral_rms() : rna_score.cc
• calc_dist() : bettercluster.cc , peptoid_rotamer_prediction_benchmark.cc , get_dihedral_peptoid.cc , get_dihedral_peptide.cc , get_dihedral_b3aa.cc
• calc_IQR() : aggregate_coarse_rna_vdw.cc
• calc_mean() : make_artificial_centroids.cc
• calc_median() : casp9_superdev.cc , sparta_superdev.cc , superdev.cc
• calc_min() : casp9_superdev.cc , sparta_superdev.cc , superdev.cc
• calc_nonlocal_segment_bb_rmsd() : domain_assemble.cc
• calc_outputCoordCsts() : minimalCstHomology.cc
• calc_prob() : SID_ERMS_prediction.cc
• calc_rama() : outputRama.cc
• calc_rama2b() : outputRama.cc
• calc_rama_scores() : torsional_potential_corrections.cc
• calc_RF() : SID_rescore.cc
• calc_rms_test() : swa_protein_main.cc
• calc_rmsd_and_clash_score() : NodePairRmsdCalculator.cc
• calc_rmsd_test() : rna_test.cc
• calc_RMSE() : SID_ERMS_prediction.cc
• calc_rmsf_and_avrg() : avrg_silent.cc
• calc_sasa() : outputLayerDesignBurial.cc , outputSasa.cc
• calc_scores() : torsional_potential_corrections.cc
• calc_sdev() : make_artificial_centroids.cc
• calc_sequence_score() : design_cycpeptide_MPI.cc
• calc_shape_complementarity() : ShapeScoring.cc
• calc_SID_score() : SID_rescore.cc
• calc_solvent_content() : cryst_reporters.hh
• calc_vm() : cryst_reporters.hh
• calculate_average_residue_scores() : HDXEnergy.cc , ResidueDisorder.cc
• calculate_backbone_sasa() : score_sidechain_sasa.cc
• calculate_binding_energy() : rnp_ddg.cc
• calculate_burial() : check_burial.cc , create_constraints.cc , homolog_cst.hh , james_util.hh , per_residue_features.cc , batch_distances.cc , template_features.cc
• calculate_disorder() : ResidueDisorder.cc
• calculate_distances() : calculate_distances.cc
• calculate_hASA_by_type_and_attractiveE() : hydrophobic_patch_stats_calculator.cc
• calculate_hASA_by_type_and_exposure() : hydrophobic_patch_stats_calculator.cc
• calculate_hASA_by_type_and_nbcount() : hydrophobic_patch_stats_calculator.cc
• calculate_helical_parameters() : extractNativeRepeats.cc
• calculate_helical_parameters_helper() : extractNativeRepeats.cc
• calculate_helical_tail_variance() : repeat_dock.cc
• calculate_hydrophobic_accessible_surface_area() : hydrophobic_patch_stats_calculator.cc
• calculate_max_rmsd_variance() : extractNativeRepeats.cc
• calculate_min_tm_variance() : extractNativeRepeats.cc
• calculate_moments() : turner_rules_test.cc
• calculate_motif_scores() : repeat_dock.cc
• calculate_order_scores() : HDXEnergy.cc , ResidueDisorder.cc
• calculate_pairwise_RMSD() : swa_rna_util.cc
• calculate_percent_disorder() : ResidueDisorder.cc
• calculate_percent_hydrophobic_distribution() : hydrophobic_patch_stats_calculator.cc
• calculate_percent_hydrophobic_stats() : hydrophobic_patch_stats_calculator.cc
• calculate_res_map() : rna_graft.cc
• calculate_rmsd_variance() : extractNativeRepeats.cc
• calculate_sasa() : calculate_sasa.cc
• calculate_sheet_pct() : extractNativeRepeats.cc
• calculate_surface_exposure() : tj_util.hh
• calculate_theoretical_RNA_length() : parin_test.cc
• calculate_theoretical_RNA_length_with_bond_angle_dependence() : parin_test.cc
• calculate_tm_variance() : extractNativeRepeats.cc
• calculate_total_hASA_within_distance_avg_values() : hydrophobic_patch_stats_calculator.cc
• calculate_total_hASA_within_distance_avgresiduevalues_allnbs_conditionalonnumnbs() : hydrophobic_patch_stats_calculator.cc
• calculate_total_hASA_within_distance_exact_hASA_values() : hydrophobic_patch_stats_calculator.cc
• calculate_total_hASA_within_distance_exact_hASA_values_allnbs() : hydrophobic_patch_stats_calculator.cc
• calculate_total_hASA_within_distance_exact_hASA_values_allnbs_exposedornot_conditionalonnumnbs() : hydrophobic_patch_stats_calculator.cc
• calculate_total_hASA_within_distance_miniSASAvalues_allnbs_exposedornot_conditionalonnumnbs() : hydrophobic_patch_stats_calculator.cc
• calculate_variations() : avrg_silent.cc
• calculateInterfaceScore() : PeptideDeriver.cc
• calpha_pdb_superimpose_pose() : david_align_and_recompute_score_and_rmsd.cc , david_align_append_and_recompute_score_and_rmsd.cc , david_darc_multirun.cc , ragul_darc_minimize.cc , simon_darc_minimize.cc , minimize_ppi.cc
• capri15_relax() : capri15.cc
• capri15_test() : capri15.cc
• capri_t033_centroid_trim_dock_test() : capri15.cc
• capri_t033_loop_test() : capri15.cc
• capri_t033_trim_dock_test() : capri15.cc
• cartesian_product() : cartesian.cc
• catch() : cenrot_jd2.cc , pcs_fragments_to_distances.cc
• CB_distance() : disulfides.hh
• cbcount_vec() : symdock_enum.cc , symdock_enum_3_1.cc , isct_test.cc
• ccd_close_loop() : fast_cm.cc
• ccd_close_zf_chainbreak() : zf_relax.cc
• ccd_loop_close() : loop_closure_test.cc
• ccd_test() : test1.cc
• cen_design() : smhybrid.cc
• cen_fold() : bpy.cc , dubois.cc , smhybrid.cc , spiro.cc
• cendnapose_from_file() : phil.hh
• cenpose_from_file() : phil.hh
• center_ca() : hubfragdesign.cc , hubabinitio.cc
• center_heavy() : hubfragdesign.cc , hubabinitio.cc
• center_of_mass() : coiled_coil_zn.cc , nisod.cc , coiled_coil.cc
• center_pose_at_origin() : cryst_design.cc
• CENTROID_DNA() : phil.hh
• centroid_rescore_test() : capri15.cc
• centroid_scores_destroys_pose() : scheme_v0_score.cc
• ch_o_pdbstats_from_pose() : pdbstats_test.cc
• chain_begin() : phil.hh
• chain_coords() : sym_multicomp_test.cc
• chain_end() : phil.hh
• chain_rmsd() : rmsd_calculator.cc
• change_docking_pose() : docking_parallel.cc
• change_floating_sc_geometry() : smhybrid.cc
• change_floating_sc_geometry_reverse() : smhybrid.cc
• check_6D_potential() : read_tensor.cc
• check_alignment_RMSD_cutoff() : swa_rna_util.cc
• check_all_poses_have_the_same_sequence() : drrafter_error_estimation.cc
• check_angle_bounds() : bettercluster.cc
• check_centroid() : mp_database_check.cc
• check_chi_correct() : easy_target_test.cc
• check_clash() : turner_rules_test.cc
• check_contact() : turner_rules_test_WORKS.cc
• check_contact_and_output() : rna_protein_test.cc
• check_coords_match() : sym_multicomp_test.cc
• check_cubic_conv_test() : check_cubic_conv.cc
• check_determinant_test() : turner_rules_test.cc
• check_filter_base_stack() : turner_rules_test.cc
• check_filter_rmsd() : stepwise_helix_test.cc
• check_for_contacts() : rna_database.cc
• check_for_contacts_and_output_jump_o2prime() : rna_database.cc
• check_for_contacts_and_output_jump_phosphate() : rna_database.cc
• check_fullatom() : mp_database_check.cc
• check_hydrophobic() : stepwise_helix_test.cc
• check_hydrophobic_contact() : stepwise_helix_test.cc
• check_inputs_for_errors() : dgdp.cc
• check_intensities() : SID_ERMS_prediction.cc
• check_interface_symmetry() : SID_ERMS_prediction.cc
• check_jump() : r_frag_quality.cc
• check_lengths() : fragment_rmsd.cc , windowed_rmsd.cc
• check_multilinear_interpolation() : read_tensor.cc
• check_number_of_poses() : ResidueDisorder.cc
• check_option_conflicts() : build_repeats.cc , helical_param.cc , ufv.cc , remodel.cc
• check_options() : mp_parameters.cc
• check_oxygen_contact_and_output() : rna_protein_test.cc
• check_pose_length() : ResidueDisorder.cc
• check_pose_size() : ResidueDisorder.cc
• check_protein_rna_clash() : rna_protein_test.cc
• check_quality_of_cluster_frags() : r_frag_quality.cc
• check_redundant() : iterhybrid_selector.cc
• check_required() : star_abinitio.cc
• check_required_options() : remodel.cc , ufv.cc , build_repeats.cc , helical_param.cc
• check_rmsd() : stepwise_helix_test.cc
• check_sequence() : ResidueDisorder.cc
• check_silent_error() : iterhybrid_selector.cc
• check_single_chain() : ResidueDisorder.cc
• check_spline() : read_tensor.cc
• check_steric_overlap() : turner_rules_test_WORKS.cc , stepwise_helix_test.cc
• check_structures() : check_rnp_coarse.cc , score_rnp_lowres.cc
• check_tensor() : read_tensor.cc
• checked_steal_fragment() : r_trjconv.cc
• checkresiduecount() : PCA_visualizer.cc
• chi_stats_test() : easy_target_test.cc
• chis_from_pose() : analyze_casp9.cc , angle_recovery_stats.cc
• choose_centroids() : kcluster.cc
• chr_chains() : helix_assembly.cc
• CIS_OMG_LOWER_RANGE() : peptoid_rotlib_test2.cc
• CIS_OMG_UPPER_RANGE() : peptoid_rotlib_test2.cc
• CIS_UPPER_TRANS_LOWER_SPLIT() : peptoid_rotlib_test2.cc
• cl_score() : cl_complex_rescore.cc
• clash() : gpu_cbdock.cc
• clash_check_bb() : gen_trimer_disulf.cc
• clash_score() : clash_score.hh
• clashcheck() : hczndimer.cc
• clashcheckhalf() : hczndimer.cc
• clean_up_database() : roc_optimizer.cc
• cleanup_dna_chains() : dna_spec_test.cc , simple_dna_regression_test.cc
• clockwise() : mpframework_test2.cc
• clone() : Svm.cc
• close_chain_breaks() : cs_rosetta_rna.cc
• close_loops() : rna_graft.cc
• cluster_outfile_test() : stepwise_test.cc , stepwise_centroid_test.cc , stepwise_template_test.cc , swa_protein_main.cc
• cluster_outfile_test_OLD() : stepwise_test.cc
• cluster_rigid_body_settings_test() : turner_rules_test.cc
• cluster_rotamers() : parin_test.cc
• cluster_rotamers_wrapper() : parin_test.cc
• cluster_silent() : dgdp.cc
• cluster_silent_file_data() : turner_rules_test.cc
• cluster_test() : rna_cluster.cc
• cmp() : pentcb_test.cc , pentcb_design.cc , CXdock_TMP.cc , pentcb.cc , dxdock.cc , dock_asym.cc , cxdock_sheet.cc , cxdesign.cc
• cmpcbc() : dxdock_movie.cc
• cmpHit() : d3_bpy_linker.cc
• cmprmsd() : CXdock.cc , dxdock_movie.cc , heterodock.cc , sicdock.cc
• cmpscnd() : sequence_tolerance_mf.cc , multistate_design_ga.cc , sequence_tolerance.cc
• cmpscore() : sicdock.cc , CXdock.cc , heterodock.cc
• cmpxsc() : dxdock_movie.cc
• cnl_print() : cnl_env_lost_hbs.cc
• cnl_store_hbs() : cnl_env_lost_hbs.cc
• cnlres_store_hbs() : cnl_env_lost_hbs.cc
• coarse_close_loop_test() : coarse_rna_test.cc
• coarse_frag_test() : coarse_rna_test.cc
• coarse_rb_test() : coarse_rna_test.cc
• coarse_rna_denovo_test() : coarse_rna_test.cc
• coarse_to_full_test() : coarse_rna_test.cc
• collect_residue_types() : restype_converter.cc
• collect_stats() : designability_stats.cc
• color_by_geom_sol_RNA_test() : rna_test.cc
• color_by_lj_base_RNA_test() : rna_test.cc
• color_by_lj_test() : stepwise_test.cc
• cols() : gpu_mat_vec.hh
• combine_refinement() : dgdp.cc
• combine_search() : dgdp.cc
• combineIdenticalLengthAln() : filterAlignments.cc
• CommonHelp() : main.cpp
• comp() : atom_tree_check.cc
• compare() : frag2profile.cc
• compare_cartesian_rmsd() : r_frag_quality.cc , r_local_rdc.cc
• compare_chi1_2_angles() : detect_tight_clusters.cc
• compare_dna_energies() : dna_spec_test.cc , simple_dna_regression_test.cc
• compare_energies() : dna_spec_test.cc , simple_dna_regression_test.cc
• compare_frags() : r_frag_quality.cc
• compare_frags_pose() : r_frag_quality.cc
• compare_gpu_result_against_cpu() : SmotifPairRmsdCalculatorGPU.CC , BundlePairRmsdCalculatorGPU.cc
• compare_residues_and_chi1_2_angles() : design_tight_clusters.cc
• compare_text_files() : diffbinder.cpp
• compare_torsion_rmsd() : r_frag_quality.cc
• compareEnergies() : evolution.cc
• compareLMAX() : symdock_enum_3_1.cc , tcdock.cc
• compile() : compile.h
• composite_sequences_from_cmd_line() : score_aln2.cc
• compute() : ligand_docking_hbonds.cc
• compute_2layer_designation() : mp_scoring_feature_reporter.cc
• compute_5layer_designation() : mp_scoring_feature_reporter.cc
• compute_bb_motif_score() : scheme_v0_score.cc
• compute_chem_shift_RMSD() : cs_rosetta_rna.cc
• compute_chi() : DisulfideTest.cc
• compute_deficit() : macrocycle_sampling.cc
• compute_folding_energies() : cartesian_ddg.cc
• compute_interface_energy() : noah_score_interface.cc
• compute_intrinsic_deviation() : r_frag_quality.cc
• compute_min_mean_rmsd_frag() : r_frag_quality.cc
• compute_motif_score() : repeat_dock.cc
• compute_num_bins() : cycgly_bbg8t3a.cc , cycgly_target.cc , cycsamp.cc
• compute_rms_and_clash_score_for_block_pair() : BundlePairRmsdCalculatorGPU.cc , SmotifPairRmsdCalculatorGPU.CC
• compute_sasa() : mp_scoring_feature_reporter.cc
• compute_sixAneighbors() : mp_scoring_feature_reporter.cc
• compute_tenAneighbors() : mp_scoring_feature_reporter.cc
• compute_twelveAneighbors() : mp_scoring_feature_reporter.cc
• compute_windowed_rama() : windowed_rama.cc
• compute_windowed_rmsd() : windowed_rmsd.cc
• concave_hull() : mpframework_test2.cc
• concave_shell() : mpframework_test2.cc
• cone_cen_nc_calculator() : per_residue_solvent_exposure.cc
• cone_FA_nc_anyatom_calculator() : per_residue_solvent_exposure.cc
• cone_FA_nc_calculator() : per_residue_solvent_exposure.cc
• cone_FA_nc_calculator_amide() : per_residue_solvent_exposure.cc
• configure_master_mover() : erraser2.cc
• connect_test() : vllb.cc
• connectivity_test() : entropy_test.cc
• constrain_loop_ends() : design_truecycpeptide_fromstub.cc , test_cyclic_rama.cc
• constraint_set_slice() : stepwise_centroid_test.cc
• contact_model_prediction() : motif_scan.cc
• contacts() : gpu_cbdock.cc
• containment_and_clash_checks() : loodo.cc
• contains_beta() : bettercluster.cc
• contourf() : gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , draw_gen_env_dep_orient_decompose.m
• converged() : optE_test.cc
• convert() : multistage_rosetta_scripts.cc
• Convert_rebuild_residue_string_to_list() : swa_rna_util.cc
• convert_silent_file_to_pose_data_list() : parin_test.cc
• convert_to_coarse_test() : coarse_rna_test.cc
• convert_to_native_test() : rna_test.cc
• convert_to_olc() : test_chain_sequence.cc
• convex_hull() : mpframework_test2.cc
• copy_asymm_unit_to_other_subunits() : count_cycpep_sequences.cc
• copy_DOFS_local() : parin_test.cc
• copy_each_residue() : partial_pose.cc , fold_tree.cc
• copy_residue_position() : design_truecycpeptide_fromstub.cc
• copy_residues() : extend.cc
• copy_rna_torsions() : rna_test.cc
• copy_rotamerized_torsions() : rna_test.cc
• copy_segment_bb() : domain_assemble.cc
• copy_using_constructor() : fold_tree.cc , partial_pose.cc
• copy_virtual_variant_type() : parin_test.cc
• copy_xyz_by_chunk() : challenge.cc
• copying_side_chains() : fold_from_loops.cc
• copying_side_chains_swap_loop() : fold_from_loops.cc
• copyresidueposition() : make_truecyclicpeptide.cc
• core_core() : gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m
• core_core_p_r_ang() : gen_env_dep_orient_draw.m
• core_core_th1() : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m
• core_core_th2() : gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• core_init_from_string() : init_util.hh
• core_init_with_additional_options() : init_util.hh
• core_surf() : gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m
• core_surf_p_r_ang() : gen_env_dep_orient_draw.m
• core_surf_th1() : gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m
• core_surf_th2() : gen_env_dep_orient.m , gen_env_dep_orient_draw.m
• correct_dunbrack() : torsional_potential_corrections.cc
• correct_rama() : torsional_potential_corrections.cc
• correlation() : ddg_benchmark.cc
• correlation_coefficient() : ddg_benchmark.cc
• cost() : alignanalyse.cc
• count_analytically() : count_cycpep_sequences.cc
• count_analytically_cyclic() : count_cycpep_sequences.cc
• count_analytically_improper_rotational() : count_cycpep_sequences.cc
• count_backbone_atoms() : make_artificial_centroids.cc
• count_bb_dihedrals() : bettercluster.cc
• count_bins() : cycpep_analysis.cc
• count_contacts() : analyze_docked_RNA_motifs.cc
• count_int_CBs_clashes() : enumeration_test.cc , matdes_dock.cc
• count_neighbors() : HDXEnergy.cc , per_residue_solvent_exposure.cc
• count_numerically() : count_cycpep_sequences.cc
• count_residue_hbonds() : hbond_connect.cc
• count_semi_analytically_improper_rotational() : count_cycpep_sequences.cc
• count_subset() : test_symmetry.cc , test_neighborhood_selector.cc
• create_and_score_fragments() : rss_energy_calculator.cc
• create_base_pair_step_database_test() : rna_database.cc
• create_bp_jump_database_test() : coarse_rna_test.cc , rna_test.cc , rna_database.cc
• create_cs_rosetta_rna_scorefxn() : cs_rosetta_rna.cc
• create_dihedral_constraint() : rna_test.cc
• create_ensemble() : ensemble_generator.cc , ensemble_generator_score12_sidechain.cc , ensemble_generator_score12_sidechain_ver2.cc
• create_extra_output() : FloppyTail_loop.cc
• create_fullcoverage_hbgeoms_to_measure() : sweep_respair_energies.cc
• create_loop() : design_truecycpeptide_fromstub.cc
• create_mingraph_for_focused_residue_pair() : sweep_respair_energies.cc
• create_MPpose() : input_from_cmd.cc , visualize_membrane.cc
• create_node_comparison_table() : BundlePairRmsdCalculatorGPU.cc
• create_pseudo_commandline() : init_util.hh
• create_random_angle_from_range() : turner_test_double_helix.cc , turner_test_one_chain.cc
• create_random_angle_from_range_list() : turner_test_double_helix.cc , turner_test_one_chain.cc
• create_random_nucleoside_torsion() : turner_test_one_chain.cc
• create_random_pose() : rna_protein_test.cc
• create_random_suite_torsion() : turner_test_one_chain.cc
• create_random_torsions() : turner_test_double_helix.cc
• create_rna_benchmark_test() : rna_test.cc
• create_rna_vall_torsions_test() : rna_test.cc , rna_database.cc
• create_schema() : sweep_respair_energies.cc
• create_score_function_from_weights_and_refEs() : optE_test.cc
• create_scorefxn() : swa_rna_util.cc , swa_rna_analytical_closure.cc
• create_starting_template() : homolog_cst.hh
• create_theozyme_pdb() : CstfileToTheozymePDB.cc
• createConstraintSet() : CycDsulf.cc
• createDihedralConstraint() : CycDsulf.cc
• createMinimizationConstraint() : CycDsulf.cc
• crossvv() : gpu_mat_vec.hh
• cs_rosetta_rna_pdb() : cs_rosetta_rna.cc
• cst_relax_test() : easy_target_test.cc
• cst_test() : dna_spec_test.cc , simple_dna_regression_test.cc
• cubic_test_function() : check_cubic_conv.cc
• cxdock_design() : cxdesign.cc , pentcb_design.cc
• cycle() : turner_rules_test.cc , coarse_rna_test.cc
• cyclic_all_atom_rms() : cycgly_canonical.cc , cycgly_superimpose.cc , gen_cyc_gly.cc , gen_cyc_gly_cst.cc
• cyclic_all_atom_rmsd() : cycgly_bbg8t3a.cc , cycgly_target.cc , cycsamp.cc
• cyclic_ca_rms() : cycgly_superimpose.cc
• cyclic_ca_rmsd() : cycgly_bbg8t3a.cc , cycgly_target.cc , cycsamp.cc
• cyclic_perm() : cycsamp.cc , gen_cyc_gly_cst.cc , gen_cyc_gly.cc , cycgly_superimpose.cc , cycgly_canonical.cc , cycgly_bbg8t3a.cc , cycgly_target.cc
• cyclic_superimpose() : gen_cyc_gly.cc , gen_cyc_gly_cst.cc , cycsamp.cc , cycgly_target.cc , cycgly_superimpose.cc , cycgly_canonical.cc , cycgly_bbg8t3a.cc
• cyclic_unique_bin() : cycgly_bbg8t3a.cc , cycgly_target.cc
• cyclize_pose() : cycgly_bbg8t3a.cc , cycgly_target.cc , cycsamp.cc
• cys_bb2m() : gpu_xforms.hh
• cys_m2bb() : gpu_xforms.hh