Here is a list of all file members with links to the files they belong to:

- c -

C : gpu_homog_atom_coords.h , functions.cc , unique_atoms.h
C1_SG : gpu_xforms.hh
C21_movx : gpu_xforms.hh
C21_rot001_COS : gpu_xforms.hh
C21_rot001_SIN : gpu_xforms.hh
C2_M : gpu_xforms.hh
C32_movx : gpu_xforms.hh
C32_rot001_COS : gpu_xforms.hh
C32_rot001_SIN : gpu_xforms.hh
C3_MY : gpu_xforms.hh
C_HI : CXdock_TMP.cc
C_LO : CXdock_TMP.cc
C_SVC : Svm.hh
c_terminal_component_list : steric_fusion_scan.cc
c_terminal_range : steric_fusion_scan.cc
CA : gpu_homog_atom_coords.h , unique_atoms.h , gpu_refold_test_cpu.hh
CA_cst_generator() : fold_from_loops.cc
CA_distance() : disulfides.hh
ca_to_allatom_main() : ca_to_allatom.cc
CAbb : gen_vdw_radius.m , gen_vdw_radius_soft.m
CaCN_ANGLE : design_truecycpeptide_fromstub.cc , test_pose_copy.cc , test_D_scoring.cc , test_cyclic_rama.cc , PCA_internal_test.cc , design_truecycpeptide_fromstub.cc , bettercluster.cc , design_cycpeptide_MPI.cc , make_truecyclicpeptide.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_peptide.cc , get_dihedral_peptoid.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
CalcCdrRmsOP : calc_cdr_rmsd.cc
CalcIrmsOP : calc_irms_despite_mismatch.cc
calculate_average_residue_scores() : HDXEnergy.cc , ResidueDisorder.cc
calculate_backbone_sasa() : score_sidechain_sasa.cc
calculate_binding_energy() : rnp_ddg.cc
calculate_burial() : create_constraints.cc , template_features.cc , batch_distances.cc , per_residue_features.cc , james_util.hh , homolog_cst.hh , check_burial.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
CapriDataOP : capri15_scoring.hh
CapriScoreType : capri15_scoring.hh
cartesian_product() : cartesian.cc
catch() : pcs_fragments_to_distances.cc , cenrot_jd2.cc
CaToAllAtomOP : ca_to_allatom.cc
CB : gen_vdw_radius.m , gen_vdw_radius_soft.m , gpu_homog_atom_coords.h , unique_atoms.h
CB_distance() : disulfides.hh
CB_P : unique_atoms.h , gpu_homog_atom_coords.h
CbCaN_to_CaNC : gpu_xforms.hh
cbcount_vec() : symdock_enum.cc , symdock_enum_3_1.cc , isct_test.cc
cbeta12 : load_tables.m
CC : gen_env_dep_orient_draw.m
ccd_close_loop() : fast_cm.cc
ccd_close_zf_chainbreak() : zf_relax.cc
ccd_loop_close() : loop_closure_test.cc
ccd_test() : test1.cc
CD : unique_atoms.h , gpu_homog_atom_coords.h
CD1 : gpu_homog_atom_coords.h , unique_atoms.h
CD1_W : gpu_homog_atom_coords.h , unique_atoms.h
CD2 : gpu_homog_atom_coords.h , unique_atoms.h
CD2_H : gpu_homog_atom_coords.h , unique_atoms.h
CD2_L : gpu_homog_atom_coords.h , unique_atoms.h
CD2_W : unique_atoms.h , gpu_homog_atom_coords.h
CD_P : gpu_homog_atom_coords.h , unique_atoms.h
CE1 : gpu_homog_atom_coords.h , unique_atoms.h
CE1_H : gpu_homog_atom_coords.h , unique_atoms.h
CE2 : gpu_homog_atom_coords.h , unique_atoms.h
CE2_W : gpu_homog_atom_coords.h , unique_atoms.h
CE3_W : gpu_homog_atom_coords.h , unique_atoms.h
CE_K : gpu_homog_atom_coords.h , unique_atoms.h
CE_M : gpu_homog_atom_coords.h , unique_atoms.h
CEN : FunGroupTK.cc
CEN_ALA : gen_vdw_radius_soft.m
CEN_ANG : FunGroupTK.cc
CEN_ARG : gen_vdw_radius_soft.m
CEN_ASN : gen_vdw_radius_soft.m
CEN_ASP : gen_vdw_radius_soft.m
CEN_AXS : FunGroupTK.cc
CEN_AXS_ORI : FunGroupTK.cc
CEN_CYS : gen_vdw_radius_soft.m
cen_design() : smhybrid.cc
cen_fold() : bpy.cc , spiro.cc , dubois.cc , smhybrid.cc
CEN_GLN : gen_vdw_radius_soft.m
CEN_GLU : gen_vdw_radius_soft.m
CEN_GLY : gen_vdw_radius_soft.m
CEN_HIS : gen_vdw_radius_soft.m
CEN_ILE : gen_vdw_radius_soft.m
CEN_LEU : gen_vdw_radius_soft.m
CEN_LYS : gen_vdw_radius_soft.m
CEN_MET : gen_vdw_radius_soft.m
CEN_PHE : gen_vdw_radius_soft.m
CEN_PRO : gen_vdw_radius_soft.m
CEN_SER : gen_vdw_radius_soft.m
CEN_THR : gen_vdw_radius_soft.m
CEN_TRP : gen_vdw_radius_soft.m
CEN_TYR : gen_vdw_radius_soft.m
CEN_VAL : gen_vdw_radius_soft.m
cendnapose_from_file() : phil.hh
cenpack : load_tables.m
cenpose_from_file() : phil.hh
CenRotCanonicalMoverOP : cenrot_jd2.cc
CenRotDockingMoverOP : cenrot_jd2.cc
CenRotRBRelaxMoverOP : cenrot_jd2.cc
CenRotRelaxMoverOP : cenrot_jd2.cc
center : mp_parameters.cc
center_ca() : hubabinitio.cc , hubfragdesign.cc
center_delta : mp_parameters.cc
center_heavy() : hubfragdesign.cc , hubabinitio.cc
center_of_mass() : coiled_coil.cc , coiled_coil_zn.cc , nisod.cc
center_pose_at_origin() : cryst_design.cc
center_search_cycles : mp_parameters.cc
center_start : mp_parameters.cc
CENTROID_DNA() : phil.hh
centroid_rescore_test() : capri15.cc
centroid_scores_destroys_pose() : scheme_v0_score.cc
cexp : functions.cc
CG : gpu_homog_atom_coords.h , unique_atoms.h
CG2 : gpu_homog_atom_coords.h , unique_atoms.h
CG_P : gpu_homog_atom_coords.h , unique_atoms.h
CH2_W : gpu_homog_atom_coords.h , unique_atoms.h
ch_o_pdbstats_from_pose() : pdbstats_test.cc
chain_begin() : phil.hh
chain_coords() : sym_multicomp_test.cc
chain_end() : phil.hh
chain_index : exposed_strand_finder.cc , InterfaceMutMaker.cc
chain_normal_angle_max : mp_parameters.cc
chain_rmsd() : rmsd_calculator.cc
chains : pdb_gen_cryst.cc , pocket_suggest_target_residues_by_ddg.cc
chains_to_compare : peptoid_rotamer_prediction_benchmark.cc
change_docking_pose() : docking_parallel.cc
change_floating_sc_geometry() : smhybrid.cc
change_floating_sc_geometry_reverse() : smhybrid.cc
char_t : core.h
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() : helical_param.cc , ufv.cc , remodel.cc , build_repeats.cc
check_rmsd : exposed_strand_finder.cc , 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() : stepwise_helix_test.cc , turner_rules_test_WORKS.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
CHI1 : plot_scoreterm.cc
CHI2 : plot_scoreterm.cc
CHI3 : plot_scoreterm.cc
CHI4 : plot_scoreterm.cc
chi_stats_test() : easy_target_test.cc
chis_from_pose() : angle_recovery_stats.cc , analyze_casp9.cc
choose_centroids() : kcluster.cc
chr_chains() : helix_assembly.cc
cimag : functions.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
clk1 : CutOutDomain.cc
clk2 : CutOutDomain.cc
clockwise() : mpframework_test2.cc
clone() : Svm.cc
close_chain_breaks() : cs_rosetta_rna.cc
close_loops() : rna_graft.cc
close_tag : Tag.cc
CloseContactWithResidueCOP : interface_ddg_bind.cc
CloseContactWithResidueOP : interface_ddg_bind.cc
ClosureMoverCOP : backbone_tests.cc
ClosureMoverOP : backbone_tests.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
ClusterCycDisulfOP : cluster_cyc_disulf.cc
cmp() : cxdesign.cc , cxdock_sheet.cc , CXdock_TMP.cc , dock_asym.cc , dxdock.cc , pentcb.cc , pentcb_design.cc , pentcb_test.cc
cmpcbc() : dxdock_movie.cc
cmpHit() : d3_bpy_linker.cc
cmplx : functions.cc
cmprmsd() : dxdock_movie.cc , heterodock.cc , sicdock.cc , CXdock.cc
cmpscnd() : sequence_tolerance_mf.cc , multistate_design_ga.cc , sequence_tolerance.cc
cmpscore() : CXdock.cc , heterodock.cc , sicdock.cc
cmpxsc() : dxdock_movie.cc
CNCa_ANGLE : design_cycpeptide_MPI.cc , test_pose_copy.cc , test_D_scoring.cc , test_cyclic_rama.cc , PCA_internal_test.cc , make_truecyclicpeptide.cc , design_truecycpeptide_fromstub.cc , bettercluster.cc
CNH_ANGLE : test_pose_copy.cc , test_D_scoring.cc , test_cyclic_rama.cc , design_truecycpeptide_fromstub.cc , PCA_internal_test.cc , design_truecycpeptide_fromstub.cc , make_truecyclicpeptide.cc , bettercluster.cc , design_cycpeptide_MPI.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
CObb : gen_vdw_radius.m , gen_vdw_radius_soft.m
COL1 : OptionCollection.cc
COL2 : OptionCollection.cc
COL3 : OptionCollection.cc
COLLECT_DATA : FixbbSimAnnealer.cc
collect_residue_types() : restype_converter.cc
collect_stats() : designability_stats.cc
color : color.h
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
ColorByLipidTypeCOP : color_by_lipid_type.cc
ColorByLipidTypeOP : color_by_lipid_type.cc
cols() : gpu_mat_vec.hh
combine_refinement() : dgdp.cc
combine_search() : dgdp.cc
combineIdenticalLengthAln() : filterAlignments.cc
command_line_argc : performance_benchmark.cc
command_line_argv : performance_benchmark.cc
comment_tag : Tag.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() : BundlePairRmsdCalculatorGPU.cc , SmotifPairRmsdCalculatorGPU.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
complex_type : SID_ERMS_prediction.cc
component_file_name : concatenate_poses.cc
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_interface_sc : InterfaceAnalyzer.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_packstat : simple_interfaceanalyzer.cc , InterfaceAnalyzer.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
conditional_t : core.h
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
CONST_ATTR : cxx_versioning_macros.hh
const_iterator : KeyLookup.functors.hh
ConstIterator : KeyLookup.functors.hh
constrain_loop_ends() : design_truecycpeptide_fromstub.cc , test_cyclic_rama.cc
constraint_set_slice() : stepwise_centroid_test.cc
ConstraintStatsMoverOP : silent_cst_quality.cc
ConstraintToolMoverCOP : r_cst_tool.cc
ConstraintToolMoverOP : r_cst_tool.cc
CONTACT_D2 : dxdock_movie.cc , pentcb_test.cc , pentcb.cc , hczndimer.cc , genP23.cc , genI213_gensym.cc , genI213_nocontacts.cc , d3_bpy_linker.cc , genI213_2comp.cc , CXdock_TMP.cc
CONTACT_DIS : CXdock_TMP.cc
contact_model_prediction() : motif_scan.cc
CONTACT_TH : hczndimer.cc , pentcb_test.cc , pentcb.cc , dxdock_movie.cc , d3_bpy_linker.cc , CXdock_TMP.cc , CXdock.cc
CONTACT_TH1 : genI213_2comp.cc , genI213_gensym.cc , genI213_nocontacts.cc , genP23.cc
CONTACT_TH2 : genI213_gensym.cc , genP23.cc , genI213_nocontacts.cc , genI213_2comp.cc
ContactMap : contactMap.cc
contacts() : gpu_cbdock.cc
containment_and_clash_checks() : loodo.cc
contains_beta() : bettercluster.cc
contourf() : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , draw_gen_env_dep_orient_decompose.m
CONV1 : draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , cal_env.m , gen_env_dep_pair.m , gen_env_dep_pair_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
Coords : dock_test.cc , PDBTest.cc , score_pdbs.cc
copy_asymm_unit_to_other_subunits() : count_cycpep_sequences.cc
copy_DOFS_local() : parin_test.cc
copy_each_residue() : fold_tree.cc , partial_pose.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 : draw_gen_env_dep_pair_decompose.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 , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , draw_matrix.m , draw_gen_env_dep_pair.m
core_core_close : draw_matrix.m
core_core_dat_r_ang : gen_env_dep_orient_draw.m
core_core_p_r_ang : gen_env_dep_orient_draw.m
core_core_sum_r : gen_env_dep_orient_draw.m
core_core_th1() : gen_env_dep_orient_decompose.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient.m
core_core_th2 : gen_env_dep_orient_draw.m , gen_env_dep_orient.m , gen_env_dep_orient_draw.m , gen_env_dep_orient.m
core_init_from_string() : init_util.hh
core_init_with_additional_options() : init_util.hh
core_surf() : draw_gen_env_dep_pair_decompose.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 , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_draw.m , draw_matrix.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m
core_surf_close : draw_matrix.m
core_surf_dat_r_ang : gen_env_dep_orient_draw.m
core_surf_p_r_ang : gen_env_dep_orient_draw.m
core_surf_sum_r : gen_env_dep_orient_draw.m
core_surf_th1 : gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , draw_gen_env_dep_orient_decompose.m , 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 , gen_env_dep_orient.m
correct_dunbrack() : torsional_potential_corrections.cc
correct_rama() : torsional_potential_corrections.cc
correlation() : ddg_benchmark.cc
correlation_coefficient() : ddg_benchmark.cc
COS_C_N_CA : gpu_refold_test_cpu.hh
COS_CA_C_N : gpu_refold_test_cpu.hh
COS_N_CA_C : gpu_refold_test_cpu.hh
cost() : alignanalyse.cc
count : gpu_octree_impl_test.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_CYCPEP_SEQUENCE_INTTYPE : count_cycpep_sequences.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_neighborhood_selector.cc , test_symmetry.cc
CovalentPeptidomimeticCreatorCOP : cov_peptidomimetic_creator.cc
CovalentPeptidomimeticCreatorOP : cov_peptidomimetic_creator.cc
CovalentPeptidomimeticDockDesignCOP : cov_hbs.cc
CovalentPeptidomimeticDockDesignOP : cov_hbs.cc
cpolar : functions.cc
creal : functions.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_database.cc , rna_test.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_EXCEPTION : Exceptions.hh
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_analytical_closure.cc , swa_rna_util.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 : gen_env_dep_orient_draw.m
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
cstring_view : os.h
CSTs : hubdenovo.cc
CUBIC : spacegroup.hh
cubic_test_function() : check_cubic_conv.cc
CustomHeader : functor_test.cpp
cutoff : gen_vdw_radius.m , gen_vdw_radius_soft.m , gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair_decompose.m
cxdock_design() : cxdesign.cc , pentcb_design.cc
CYAN : capri15_scoring.hh
cycle() : coarse_rna_test.cc , turner_rules_test.cc
cyclic : cyclic_pack.cc , get_dihedral_peptide.cc , get_dihedral_peptoid.cc , peptoid_rotamer_prediction_benchmark.cc
cyclic_all_atom_rms() : gen_cyc_gly.cc , gen_cyc_gly_cst.cc , cycgly_superimpose.cc , cycgly_canonical.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() : cycgly_superimpose.cc , gen_cyc_gly_cst.cc , gen_cyc_gly.cc , cycsamp.cc , cycgly_canonical.cc , cycgly_bbg8t3a.cc , cycgly_target.cc
cyclic_superimpose() : cycgly_bbg8t3a.cc , cycgly_canonical.cc , cycgly_superimpose.cc , cycgly_target.cc , cycsamp.cc , gen_cyc_gly.cc , gen_cyc_gly_cst.cc
cyclic_unique_bin() : cycgly_target.cc , cycgly_bbg8t3a.cc
cyclize_pose() : cycgly_bbg8t3a.cc , cycgly_target.cc , cycsamp.cc
CYS : gen_env_dep_orient_draw.m , hczndimer.cc , gen_vdw_radius.m , load_pair_env_table.m , load_angle_r_table.m , gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_orient_decompose.m , load_pair_env_table_ref.m , load_pair_env_table.m , cal_env.m , draw_matrix.m , draw_gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m
CYS_1oSIN_CB_SG_HG : FunGroupTK.cc
cys_bb2m() : gpu_xforms.hh
CYS_CB_HG_DIS : FunGroupTK.cc
CYS_CB_SG_BLEN : FunGroupTK.cc
CYS_CB_SG_PERP : FunGroupTK.cc
CYS_HG_SG_PRJLEN : FunGroupTK.cc
CYS_HG_SG_X_DROP : FunGroupTK.cc
cys_m2bb() : gpu_xforms.hh
CYS_SG_CB_H : FunGroupTK.cc
CYSPOS : CycDsulf.cc
CZ : gpu_homog_atom_coords.h , unique_atoms.h
CZ2_W : gpu_homog_atom_coords.h , unique_atoms.h
CZ3_W : gpu_homog_atom_coords.h , unique_atoms.h
CZ_R : gpu_homog_atom_coords.h , unique_atoms.h