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

- c -

• c : core::pack::dunbrack
• C : protocols::forge::build::SegmentInsertConnectionScheme
• c2n : protocols::rigid
• C_ALA : protocols::match
• C_CAR : protocols::match
• C_METHYLAMIDATION : core::chemical
• C_pi_sp2 : core::chemical::orbitals
• CA : protocols::frag_picker , protocols::sic_dock
• CA_gdtmm() : core::scoring
• CA_maxsub() : core::scoring
• CA_maxsub_by_subset() : core::scoring
• CA_rmsd() : core::scoring
• CA_rmsd_symmetric() : core::scoring
• CA_superimpose() : protocols::toolbox
• CaCbCb_Angle_FuncAP : core::scoring::disulfides
• CaCbCb_Angle_FuncCAP : core::scoring::disulfides
• CaCbCb_Angle_FuncCOP : core::scoring::disulfides
• CaCbCb_Angle_FuncOP : core::scoring::disulfides
• CaCbCbCa_Dihedral_FuncAP : core::scoring::disulfides
• CaCbCbCa_Dihedral_FuncCAP : core::scoring::disulfides
• CaCbCbCa_Dihedral_FuncCOP : core::scoring::disulfides
• CaCbCbCa_Dihedral_FuncOP : core::scoring::disulfides
• CacheableAtomID_MapVectorAP : core::id
• CacheableAtomID_MapVectorCAP : core::id
• CacheableAtomID_MapVectorCOP : core::id
• CacheableAtomID_MapVectorOP : core::id
• CacheableAtomPairFuncMapCOP : core::scoring::custom_pair_distance
• CacheableAtomPairFuncMapOP : core::scoring::custom_pair_distance
• CacheableObserverAP : core::pose::datacache
• CacheableObserverCAP : core::pose::datacache
• CacheableObserverCOP : core::pose::datacache
• CacheableObserverOP : core::pose::datacache
• CacheablePoseRawPtrAP : core::pose::datacache
• CacheablePoseRawPtrCAP : core::pose::datacache
• CacheablePoseRawPtrCOP : core::pose::datacache
• CacheablePoseRawPtrOP : core::pose::datacache
• CacheableSequenceProfileAP : core::sequence
• CacheableSequenceProfileCAP : core::sequence
• CacheableSequenceProfileCOP : core::sequence
• CacheableSequenceProfileOP : core::sequence
• CachingScoringMethodCOP : protocols::frag_picker::scores
• CachingScoringMethodOP : protocols::frag_picker::scores
• calc_all_averages() : protocols::unfolded_state_energy_calculator
• calc_all_dist() : protocols::MakeRotLib
• calc_atom_masks() : core::scoring
• calc_centroids() : protocols::MakeRotLib
• calc_delta_sasa() : protocols::fldsgn::topology
• calc_dist() : protocols::MakeRotLib
• calc_fit_R() : protocols::toolbox
• calc_Fnat() : protocols::docking
• calc_interacting_vector() : core::pack::task::operation::util
• calc_interaction_energy() : protocols::docking
• calc_interface_vector() : core::pack::task::operation::util
• calc_Irmsd() : protocols::docking
• calc_Lrmsd() : protocols::docking
• calc_pareto_front() : protocols::design_opt
• calc_per_atom_sasa() : core::scoring
• calc_per_res_hydrophobic_sasa() : core::scoring
• calc_per_residue_scores() : protocols::sparta
• calc_res_contact() : protocols::docking
• calc_rotamer_clusters() : protocols::MakeRotLib
• calc_std_dev() : protocols::MakeRotLib
• calc_strand_pairing_set() : protocols::fldsgn::topology
• calc_total_sasa() : core::scoring
• calc_vector_boltzmann() : protocols::unfolded_state_energy_calculator
• calc_vector_mean() : protocols::unfolded_state_energy_calculator
• calc_vector_median() : protocols::unfolded_state_energy_calculator
• calc_vector_mode() : protocols::unfolded_state_energy_calculator
• calculate_carbohydrate_phi() : core::pose::carbohydrates
• calculate_ccd_angle() : protocols::loops::loop_closure::ccd
• CalculatorFilterCOP : protocols::filters
• CalculatorFilterOP : protocols::filters
• CALIBRATION_ATOM_TYPE : protocols::noesy_assign
• CalibrationTypeCumulator : protocols::noesy_assign
• calpha_superimpose_pose() : core::scoring
• calpha_superimpose_with_mapping() : core::sequence
• camelid_last_loop : protocols::antibody2
• CANCEL_BATCH : protocols::jd2::archive
• Candidate : protocols::frag_picker , protocols::frag_picker::nonlocal
• Candidates : protocols::frag_picker
• CandidatesCollectorCOP : protocols::frag_picker
• CandidatesCollectorOP : protocols::frag_picker
• CandidatesSink : protocols::frag_picker
• canonical_atom_count() : core::pose
• canonical_residue_count() : core::pose
• canonical_sampling_main() : protocols::canonical_sampling
• CanonicalSamplingMoverCOP : protocols::canonical_sampling , protocols::moves
• CanonicalSamplingMoverOP : protocols::canonical_sampling , protocols::moves
• carbohydrate_phi_offset_from_BB() : core::pose::carbohydrates
• CarbohydrateInfoCOP : core::chemical::carbohydrates
• CarbohydrateInfoOP : core::chemical::carbohydrates
• CarbonHBondEnergyCreator_registrator : core
• CarbonHBondPotentialCOP : core::scoring::carbon_hbonds
• CarbonHBondPotentialOP : core::scoring::carbon_hbonds
• CARBOXYLATION : core::chemical
• Caro : core::chemical::sdf
• CArray_Energy : core::scoring
• CArray_TableEnergy : core::scoring
• CArrayP_Energy : core::scoring
• CArrayP_TableEnergy : core::scoring
• cart_bonded : core::scoring
• cart_bonded_angle : core::scoring
• cart_bonded_length : core::scoring
• cart_bonded_lr : core::scoring::methods
• cart_bonded_torsion : core::scoring
• cart_numerical_derivative_check() : core::optimization
• CartBondedParametersAP : core::scoring::methods
• CartBondedParametersCAP : core::scoring::methods
• CartBondedParametersCOP : core::scoring::methods
• CartBondedParametersOP : core::scoring::methods
• cartesian_collect_atompairE_deriv() : core::optimization
• cartesian_collect_torsional_deriv() : core::optimization
• cartesian_dfunc() : core::optimization
• CartesianBondedEnergyAP : core::scoring::methods
• CartesianBondedEnergyCAP : core::scoring::methods
• CartesianBondedEnergyCOP : core::scoring::methods
• CartesianBondedEnergyCreator_registrator : core
• CartesianBondedEnergyOP : core::scoring::methods
• CartesianHybridizeCOP : protocols::hybridization
• CartesianHybridizeOP : protocols::hybridization
• CartesianMinimizerCOP : core::optimization
• CartesianMinimizerMapCOP : core::optimization
• CartesianMinimizerMapOP : core::optimization
• CartesianMinimizerOP : core::optimization
• CartesianSamplerCOP : protocols::hybridization
• CartesianSamplerOP : protocols::hybridization
• CartSCMinMinimizerMapCOP : core::pack::scmin
• CartSCMinMinimizerMapOP : core::pack::scmin
• CartSCMinMultifuncCOP : core::pack::scmin
• CartSCMinMultifuncOP : core::pack::scmin
• case_from_lines() : core::chemical
• catalytic_res() : protocols::enzdes::enzutil
• CavBallCIter : core::scoring::packstat
• CavBallIter : core::scoring::packstat
• CavBalls : core::scoring::packstat
• cavity_distance_constraint() : core::scoring::packstat
• CB : protocols::frag_picker , protocols::sic_dock
• CB_Angle_FuncOP : core::scoring::disulfides
• Cb_Distance_FuncAP : core::scoring::disulfides
• Cb_Distance_FuncCAP : core::scoring::disulfides
• Cb_Distance_FuncCOP : core::scoring::disulfides
• Cb_Distance_FuncOP : core::scoring::disulfides
• cb_weight() : protocols::sic_dock
• cb_weight_map_from_pose() : protocols::sic_dock
• cb_weights_from_pose() : protocols::sic_dock
• cbeta : core::scoring
• cbeta_smooth : core::scoring
• cbeta_vector() : core::pack::task::operation::util
• CBScoreCOP : protocols::sic_dock
• CBScoreOP : protocols::sic_dock
• CBSG_Dihedral_FuncOP : core::scoring::disulfides
• ccd_close_loops() : protocols::loops
• ccd_moves() : protocols::loops::loop_closure::ccd
• CcdLoopClosureMoverCOP : protocols::loops::loop_closure::ccd
• CcdLoopClosureMoverOP : protocols::loops::loop_closure::ccd
• CcdMoverCOP : protocols::loops::loop_closure::ccd
• CcdMoverOP : protocols::loops::loop_closure::ccd
• CCDMoveWrapperOP : protocols::rbsegment_relax
• CCP4HDSIZE : core::scoring::electron_density , core::scoring::electron_density_atomwise
• cd_1b : core::scoring::methods
• cd_2b : core::scoring::methods
• cd_lr_2b : core::scoring::methods
• CDFr : protocols::fldsgn::topology
• Cdouble : core::chemical::sdf
• CDR_H3_cter_filter() : protocols::antibody2
• CDR_H3_filter_legacy_code_with_old_rule() : protocols::antibody2
• CDRH3ModelerCOP : protocols::antibody
• CDRH3ModelerOP : protocols::antibody
• CDRsMinPackMinCOP : protocols::antibody2
• CDRsMinPackMinOP : protocols::antibody2
• CellOP : core::sequence
• CEN : protocols::frag_picker , protocols::kinmatch
• CEN_ANG : protocols::kinmatch
• CEN_AXS : protocols::kinmatch
• CEN_AXS_ORI : protocols::kinmatch
• Cen_Distance_FuncAP : core::scoring::disulfides
• Cen_Distance_FuncCAP : core::scoring::disulfides
• Cen_Distance_FuncCOP : core::scoring::disulfides
• Cen_Distance_FuncOP : core::scoring::disulfides
• CEN_DOCK_SCORE : core::conformation::symmetry
• cen_env_smooth : core::scoring
• cen_hb : core::scoring
• cen_pair_smooth : core::scoring
• CenHBEnergyCreator_registrator : core
• CenHBPotentialCOP : core::scoring
• CenHBPotentialOP : core::scoring
• CenListInfoOP : core::scoring
• cenpack : core::scoring
• cenpack_smooth : core::scoring
• CenPairEnergyCreator_registrator : core
• center_of_mass() : protocols::geometry
• CENTROID : core::chemical
• centroid_disulfide_energy : core::scoring::methods
• CENTROID_HA : core::chemical
• centroid_neighbor_graph : core::scoring
• centroid_pair_by_jump() : protocols::geometry
• centroid_pose_from_pdb() : core::import_pose
• CENTROID_WTS : core::scoring
• CentroidDisulfideEnergyContainerAP : core::scoring::disulfides
• CentroidDisulfideEnergyContainerCAP : core::scoring::disulfides
• CentroidDisulfideEnergyContainerCOP : core::scoring::disulfides
• CentroidDisulfideEnergyContainerOP : core::scoring::disulfides
• CentroidDisulfideEnergyCOP : core::scoring::disulfides
• CentroidDisulfideEnergyCreator_registrator : core
• CentroidDisulfideEnergyOP : core::scoring::disulfides
• CentroidDisulfidePotentialAP : core::scoring::disulfides
• CentroidDisulfidePotentialCAP : core::scoring::disulfides
• CentroidDisulfidePotentialCOP : core::scoring::disulfides
• CentroidDisulfidePotentialOP : core::scoring::disulfides
• CentroidRelaxAP : protocols::relax
• CentroidRelaxCAP : protocols::relax
• CentroidRelaxCOP : protocols::relax
• CentroidRelaxMoverOP : protocols::surface_docking
• CentroidRelaxOP : protocols::relax
• centroids_by_jump() : protocols::geometry
• centroids_by_jump_int() : protocols::geometry
• CFr : protocols::fldsgn::topology
• ch_bond : core::scoring
• ch_bond_bb_bb : core::scoring
• ch_bond_bb_sc : core::scoring
• ch_bond_sc_sc : core::scoring
• CHAIN_COLOR : protocols::viewer::graphics_states_param
• CHAIN_TERMINUS_3PRIME : protocols::swa::monte_carlo
• CHAIN_TERMINUS_5PRIME : protocols::swa::monte_carlo
• chainbreak : core::scoring
• CHAINBREAK_BOGUS_ATOM_ID : core::id
• CHAINBREAK_BOGUS_NAMED_ATOM_ID : core::id
• CHAINBREAK_SCORE_RAMP_FACTOR : protocols::loops::loop_mover::refine
• CHAINBREAK_WEIGHT() : protocols::anchored_design
• ChainbreakEnergyCreator_registrator : core
• chainID : protocols::loops
• ChainIsCreator_registrator : core
• ChainIsntCreator_registrator : core
• ChainIsntOP : core::pack::task::operation
• ChainIsOP : core::pack::task::operation
• change_cys_state() : core::conformation
• ChangeFoldTreeMoverCOP : protocols::moves
• ChangeFoldTreeMoverOP : protocols::moves
• Charge : core
• ChargeChargeFeaturesCOP : protocols::features
• ChargeChargeFeaturesOP : protocols::features
• chco : core::scoring::rna::chemical_shift
• check_all_ligand_atoms() : protocols::ligand_docking::ligand_options
• check_base_pair() : protocols::rna
• check_binary_chars() : core::io::serialization
• check_binary_unsigned_int() : core::io::serialization
• Check_chain_closable() : protocols::swa::rna
• Check_chain_closable_floating_base() : protocols::swa::rna
• check_deprecated_flags() : core
• check_domain_map() : core::pose
• check_floating_base_chain_closable() : protocols::swa::rna
• check_for_messed_up_structure() : protocols::swa::rna
• check_good_neighbor() : core::conformation
• check_hbonds : core::optimization::symmetry
• check_in_base_pair_list() : protocols::rna
• check_internal_hbonds() : protocols::fldsgn::topology
• check_is_working_res() : protocols::swa::rna
• check_kink_helix() : protocols::fldsgn::topology
• check_neighbor_ligand_atom() : protocols::ligand_docking::ligand_options
• check_overlap_pos() : protocols::loops::loop_closure::ccd
• check_rama : core::optimization::symmetry
• check_required() : protocols::star
• check_required_cm() : protocols::medal
• check_required_common() : protocols::medal
• check_RMSD() : protocols::ligand_docking
• check_score() : protocols::ligand_docking
• check_score_components : core::optimization::symmetry
• check_score_components_verbose : core::optimization::symmetry
• check_scorefxn_has_constraint_terms_if_pose_has_constraints() : protocols::swa
• check_surface_area_leerichards_deriv() : core::scoring::packstat
• check_torsions() : protocols::loops::loop_closure::ccd
• check_validity_and_get_working_res() : protocols::swa::rna
• checkpoint_cleanup() : protocols::dna
• checkpoint_with_interval() : protocols::checkpoint
• CheckPointerCOP : protocols::checkpoint
• CheckPointerOP : protocols::checkpoint
• ChemicalShiftAnisotropyCOP : core::scoring
• ChemicalShiftAnisotropyEnergyCreator_registrator : core
• ChemicalShiftAnisotropyEnergyOP : core::scoring::methods
• ChemicalShiftAnisotropyOP : core::scoring
• ChemicalShiftSequenceCOP : core::sequence
• ChemicalShiftSequenceOP : core::sequence
• CHI : core::id , core::scoring::dna , core::scoring::rna
• CHI1 : core::scoring
• chi1_torsion_atom() : core::scoring::rna
• chi1_torsion_atom_index() : core::scoring::rna
• CHI2 : core::scoring
• chi2_torsion_atom_index() : core::scoring::hackaro
• CHI3 : core::scoring
• CHI4 : core::scoring
• chi_continuation() : core::conformation
• chi_interruption() : core::conformation
• Chirality : protocols::simple_moves::chiral
• ChiralMoverCOP : protocols::simple_moves::chiral
• ChiralMoverOP : protocols::simple_moves::chiral
• chis_from_pose() : protocols::comparative_modeling
• ChiSetCOP : core::pack::dunbrack
• ChiSetOP : core::pack::dunbrack
• ChiStrategy : protocols::match::upstream
• ChiVector : core::pack::dunbrack
• choose_effective_sequence_separation() : core::scoring::constraints
• chop_fragments() : core::fragment
• Chothia : protocols::antibody2
• chr_chains() : core::io::pdb , core::pose
• chrg : core::scoring::rna::chemical_shift
• chunk_probabilities() : protocols::medal
• ChunkCOP : protocols::nonlocal
• ChunkOP : protocols::nonlocal
• chunks_by_CA_CA_distance() : protocols::nonlocal
• ChunkSetOP : protocols::rna
• ChunkTrialMoverCOP : protocols::hybridization
• ChunkTrialMoverOP : protocols::hybridization
• ci_1b : core::scoring::methods
• ci_2b : core::scoring::methods
• CI_geom_sol : core::scoring
• CI_geom_sol_intra_RNA : core::scoring
• ci_lr_2b : core::scoring::methods
• CircleIter : core::scoring::packstat
• Circles : core::scoring::packstat
• CircularGeneral1D_FuncCOP : core::scoring::constraints
• CircularGeneral1D_FuncOP : core::scoring::constraints
• CircularHarmonicFuncCOP : core::scoring::constraints
• CircularHarmonicFuncOP : core::scoring::constraints
• CircularPermutation_AP : protocols::fldsgn
• CircularPermutation_CAP : protocols::fldsgn
• CircularPermutation_COP : protocols::fldsgn
• CircularPermutation_OP : protocols::fldsgn
• CircularPowerFuncCOP : core::scoring::constraints
• CircularPowerFuncOP : core::scoring::constraints
• CircularSigmoidalFuncCOP : core::scoring::constraints
• CircularSigmoidalFuncOP : core::scoring::constraints
• ClaimerMessageAP : protocols::topology_broker
• ClaimerMessageCAP : protocols::topology_broker
• ClaimerMessageCOP : protocols::topology_broker
• ClaimerMessageOP : protocols::topology_broker
• ClassicAbinitioCOP : protocols::abinitio
• ClassicAbinitioOP : protocols::abinitio
• ClassicFragmentMoverCOP : protocols::simple_moves
• ClassicFragmentMoverOP : protocols::simple_moves
• ClassicMatchAlgorithmCOP : protocols::match::downstream
• ClassicMatchAlgorithmOP : protocols::match::downstream
• classify_base_pairs() : protocols::rna
• clear_conformation_viewers() : protocols::viewer
• CLEAR_IF_CACHING_FRAGMENTS : protocols::forge::components::VLB_VallMemoryUsage
• clearPoseExtraScore() : core::pose
• clearPoseExtraScores() : core::pose
• clone() : core::io::serialization
• close_chainbreaks() : protocols::jumping
• close_to_dna() : protocols::dna
• closed_range() : protocols::forge::methods
• CloseOneCDRLoopCOP : protocols::antibody2
• CloseOneCDRLoopOP : protocols::antibody2
• CloseOneMoverCOP : protocols::antibody
• CloseOneMoverOP : protocols::antibody
• closest_larger_peptide_vertex() : protocols::forge::methods
• closest_smaller_peptide_vertex() : protocols::forge::methods
• CloudPDBWriterCOP : protocols::match::output
• CloudPDBWriterOP : protocols::match::output
• cluster_silent_structs() : protocols::toolbox
• ClusterBaseCOP : protocols::cluster
• ClusterBaseOP : protocols::cluster
• ClusterPhilStyleCOP : protocols::cluster
• ClusterPhilStyleOP : protocols::cluster
• cm_main() : protocols::comparative_modeling
• cmp() : protocols::loophash
• cmp_pair_by_first_vec_val() : protocols::design_opt
• cmp_pair_by_second() : protocols::design_opt
• cmp_pair_vec_by_first_vec_val() : protocols::design_opt
• cmp_particles() : core::optimization
• co : core::scoring
• coarse_beadlj : core::scoring
• coarse_fa_atr : core::scoring
• coarse_fa_rep : core::scoring
• coarse_fa_sol : core::scoring
• COARSE_RNA() : core::chemical
• COARSE_TWO_BEAD : core::chemical
• CoarseEtableAP : core::coarse
• CoarseEtableCAP : core::coarse
• CoarseEtableCOP : core::coarse
• CoarseEtableOP : core::coarse
• CoarseRNA_LoopCloserOP : protocols::coarse_rna
• CoarseRotamerCOP : core::pack::dunbrack
• CoarseRotamerOP : core::pack::dunbrack
• CoarseRotamerSetCOP : core::pack::dunbrack
• CoarseRotamerSetOP : core::pack::dunbrack
• CoarseSingleResidueLibraryCOP : core::pack::dunbrack
• CoarseSingleResidueLibraryOP : core::pack::dunbrack
• ColorMode : protocols::viewer::graphics_states_param
• combinable() : core::scoring::constraints
• combine_and_trim() : protocols::nonlocal
• combine_constraints() : core::scoring::constraints
• combine_loops() : protocols::medal
• combine_NMR_atom_string() : core::scoring::constraints
• combine_sequence_mappings() : core::id
• combine_two_poses() : protocols::seeded_abinitio
• CombineChainsMoverCOP : protocols::domain_assembly
• CombineChainsMoverOP : protocols::domain_assembly
• CombinedFilterCOP : protocols::filters
• CombinedFilterOP : protocols::filters
• CombinedTaskOperationOP : protocols::flxbb
• comma_strings_to_map() : core::conformation::symmetry
• comma_strings_to_vector() : core::conformation::symmetry
• comma_strings_to_vector_map() : core::conformation::symmetry
• comment_begin() : core::pack::task
• common_setup() : protocols::abinitio
• compare() : protocols::fldsgn::topology
• compare_atom_coordinates() : core::pose
• compare_binary_protein_silent_struct() : core::pose
• compare_by_abs() : core::scoring
• compare_mingraph_and_energy_graph() : core::pack
• compare_RNA_char() : protocols::rna
• compare_RNA_secstruct() : protocols::rna
• compare_simple_inteaction_graph_alt_state_and_energy_graph() : core::pack
• compareIndexEnergyPair() : protocols::cluster , protocols::toolbox
• CompareQueryPositionCOP : protocols::frag_picker
• CompareQueryPositionOP : protocols::frag_picker
• compareRef_fxn() : protocols::sparta
• CompareScoreComponentCOP : protocols::frag_picker
• CompareScoreComponentOP : protocols::frag_picker
• CompareTotalScoreCOP : protocols::frag_picker
• CompareTotalScoreOP : protocols::frag_picker
• complete_connections_tracer() : protocols::ligand_docking
• CompositeScoringSchemeOP : core::sequence
• CompositeSegment : protocols::rbsegment_relax
• CompositeSequenceCOP : core::sequence
• CompositeSequenceCreator_registrator : core
• CompositeSequenceOP : core::sequence
• CompositionMoverCOP : protocols::moves
• CompositionMoverOP : protocols::moves
• CompoundFilterCOP : protocols::filters
• CompoundFilterOP : protocols::filters
• compute_and_store_pose_waters() : core::scoring::methods
• compute_atom_packing_scores() : core::scoring::packstat
• compute_avge_scores() : protocols::sasa_scores
• compute_bb_centroid() : core::scoring
• compute_bb_radius() : core::scoring
• compute_cav_ball_clusters() : core::scoring::packstat
• compute_cav_ball_neighbor_count() : core::scoring::packstat
• compute_cav_ball_volumes() : core::scoring::packstat
• compute_coefficients() : core::scoring::electron_density::SplineInterp
• compute_dec15_score() : core::scoring::packing
• compute_exact_geosol() : core::scoring::geometric_solvation
• compute_holes_deriv() : core::scoring::packing
• compute_holes_deriv_res() : core::scoring::packing
• compute_holes_score() : core::scoring::packing
• compute_holes_score_res() : core::scoring::packing
• compute_holes_surfs() : core::scoring::packing
• compute_jump_rmsd() : core::scoring
• compute_packing_score() : core::scoring::packstat
• compute_packing_score_leerichards() : core::scoring::packstat
• compute_per_residue_coverage() : core::fragment
• compute_per_residue_probabilities() : protocols::star
• compute_residue_packing_score() : core::scoring::packstat
• compute_residue_packing_scores() : core::scoring::packstat
• compute_residue_sasas_for_sasa_scores() : protocols::sasa_scores
• compute_rosettaholes_score() : core::scoring::packing
• compute_sasa() : core::scoring::packstat
• compute_sasa_generic() : core::scoring::packstat
• compute_sasapack_scores() : protocols::sasa_scores
• compute_sc_centroid() : core::scoring
• compute_sc_radius() : core::scoring
• compute_smooth_nb_deriv() : core::scoring::packing
• compute_ss_regions() : protocols::loops
• compute_surface_area_leerichards() : core::scoring::packstat
• compute_surface_area_leerichards_deriv() : core::scoring::packstat
• compute_surrounding_sasa() : core::scoring::packstat
• concatenate_profiles() : protocols::protein_interface_design::movers
• ConcurrencyTestCOP : protocols::features::helixAssembly
• ConcurrencyTestOP : protocols::features::helixAssembly
• conf2pdb_chain() : core::pose
• configure_rmc() : protocols::star
• ConformationCOP : core::conformation
• ConformationKinWriterCOP : core::conformation
• ConformationKinWriterOP : core::conformation
• ConformationOP : core::conformation
• ConformationViewerOP : protocols::viewer
• conformerMove : protocols::ligand_docking
• ConformerSwitchMoverCOP : protocols::docking
• ConformerSwitchMoverOP : protocols::docking
• connect_from() : protocols::protein_interface_design::movers
• connect_to() : protocols::protein_interface_design::movers
• connected_mainchain_atomids() : protocols::backrub
• connection_indices() : core::scoring::mm
• ConnectRightAP : protocols::forge::build
• ConnectRightCAP : protocols::forge::build
• ConnectRightCOP : protocols::forge::build
• ConnectRightOP : protocols::forge::build
• connects_rigid_regions() : protocols::topology_broker
• ConsensusDesignMoverOP : protocols::simple_moves
• ConservedPosMutationFilterCOP : protocols::simple_filters
• ConservedPosMutationFilterOP : protocols::simple_filters
• const_sub_to_full_info_from_pose() : protocols::swa::monte_carlo
• ConstAbinitioMoverWeightAP : protocols::topology_broker::weights
• ConstAbinitioMoverWeightCAP : protocols::topology_broker::weights
• ConstAbinitioMoverWeightCOP : protocols::topology_broker::weights
• ConstAbinitioMoverWeightOP : protocols::topology_broker::weights
• constant_constraint : core::scoring
• ConstantFuncOP : core::scoring::constraints
• ConstantLengthFragSetCOP : core::fragment
• ConstantLengthFragSetOP : core::fragment
• constrain_ligand_torsions() : protocols::ligand_docking
• constrain_pose_res_to_invrots() : protocols::toolbox::match_enzdes_util
• constrained_optimization_weight_func : protocols::optimize_weights
• constraint_set_slice() : protocols::swa
• ConstraintClaimerAP : protocols::topology_broker
• ConstraintClaimerCAP : protocols::topology_broker
• ConstraintClaimerCOP : protocols::topology_broker
• ConstraintClaimerOP : protocols::topology_broker
• ConstraintCOP : core::scoring::constraints
• ConstraintCOPs : core::scoring::constraints
• ConstraintCreatorCOP : core::scoring::constraints
• ConstraintCreatorOP : core::scoring::constraints
• ConstraintedOptimizationWeightFuncOP : protocols::optimize_weights
• ConstraintEvaluatorCOP : protocols::constraints_additional
• ConstraintEvaluatorOP : protocols::constraints_additional
• ConstraintEvaluatorWrapperAP : protocols::topology_broker
• ConstraintEvaluatorWrapperCAP : protocols::topology_broker
• ConstraintEvaluatorWrapperCOP : protocols::topology_broker
• ConstraintEvaluatorWrapperOP : protocols::topology_broker
• ConstraintFileRCGCAP : protocols::forge::constraints
• ConstraintFileRCGOP : protocols::forge::constraints
• ConstraintFragmentSamplerOP : protocols::abinitio
• ConstraintGraphCOP : core::scoring::constraints
• ConstraintGraphOP : core::scoring::constraints
• ConstrainToIdealMoverCOP : protocols::simple_moves
• ConstrainToIdealMoverOP : protocols::simple_moves
• ConstraintOP : core::scoring::constraints
• ConstraintOPs : protocols::flxbb , core::scoring::constraints
• constraints_lr : core::scoring::methods
• constraints_NtoC() : protocols::flxbb
• constraints_sheet() : protocols::flxbb
• ConstraintsCOP : core::scoring::constraints
• ConstraintScoreCutoffFilterCOP : protocols::simple_filters
• ConstraintScoreCutoffFilterOP : protocols::simple_filters
• ConstraintsEnergyCOP : core::scoring::constraints
• ConstraintsEnergyCreator_registrator : core
• ConstraintsEnergyOP : core::scoring::constraints
• ConstraintSetCOP : core::scoring::constraints
• ConstraintSetMoverCOP : protocols::simple_moves
• ConstraintSetMoverOP : protocols::simple_moves
• ConstraintSetOP : core::scoring::constraints
• ConstraintsOP : core::scoring::constraints
• construct_poly_ala_pose() : protocols::toolbox::pose_manipulation
• construct_poly_uniq_restype_pose() : protocols::toolbox::pose_manipulation
• construct_poly_XXX_pose() : protocols::toolbox::pose_manipulation
• contact_distance2() : protocols::dna
• contact_name() : protocols::frag_picker
• contact_type() : protocols::frag_picker
• ContactCOP : protocols::frag_picker
• ContactCountsCOP : protocols::frag_picker
• ContactCountsOP : protocols::frag_picker
• ContactMapCOP : protocols::contact_map
• ContactMapOP : protocols::contact_map
• ContactOP : protocols::frag_picker
• ContactOrderEnergyCreator_registrator : core
• ContactPartnerAP : protocols::contact_map
• CONTACTS : core::conformation::symmetry
• ContactType : protocols::frag_picker
• Contain_residue_at_seq_num() : protocols::swa::rna
• Contain_seq_num() : core::scoring::rna::chemical_shift , protocols::swa , protocols::swa::rna
• contains() : protocols::sparta
• contains_stageid() : protocols::abinitio
• ContextDependentLRTwoBodyEnergyCOP : core::scoring::methods
• ContextDependentLRTwoBodyEnergyOP : core::scoring::methods
• ContextDependentOneBodyEnergyOP : core::scoring::methods
• ContextDependentTwoBodyEnergyCOP : core::scoring::methods
• ContextDependentTwoBodyEnergyOP : core::scoring::methods
• ContextGraphCOP : core::scoring
• ContextGraphOP : core::scoring
• ContextGraphType : core::scoring
• ContextIndependentGeometricSolEnergyCreator_registrator : core
• ContextIndependentLRTwoBodyEnergyCOP : core::scoring::methods
• ContextIndependentLRTwoBodyEnergyOP : core::scoring::methods
• ContextIndependentOneBodyEnergyCOP : core::scoring::methods
• ContextIndependentOneBodyEnergyOP : core::scoring::methods
• ContextIndependentTwoBodyEnergyCOP : core::scoring::methods
• ContextIndependentTwoBodyEnergyOP : core::scoring::methods
• ContingentFilterCOP : protocols::filters
• ContingentFilterOP : protocols::filters
• ContinuousRotamerSetCOP : core::pack::rotamer_set
• ContinuousRotamerSetOP : core::pack::rotamer_set
• ContinuousRotamerSetsCOP : core::pack::rotamer_set
• ContinuousRotamerSetsOP : core::pack::rotamer_set
• ConvergenceCheckCOP : protocols::moves::mc_convergence_checks
• ConvergenceCheckOP : protocols::moves::mc_convergence_checks
• convert_acgu_to_1234() : core::scoring::rna
• convert_atom_name() : core::io::pdb
• convert_based_on_match_type() : protocols::rna
• convert_cartesian_to_spherical_coor_triplet() : protocols::pockets
• convert_euler_to_coordinate_matrix() : protocols::swa::rna
• convert_inorder_table_to_original_order() : core::scoring::trie
• convert_inorder_vector_to_original_order() : core::scoring::trie
• Convert_rebuild_residue_string_to_list() : protocols::swa::rna
• convert_res_name() : core::io::pdb
• convert_spherical_coor_triplet_to_cartesian() : protocols::pockets
• convert_to_working_res() : protocols::swa
• ConvertToInterpolationCoefficients() : core::scoring::electron_density::SplineInterp
• coordinate_constrain_selection() : protocols::relax
• coordinate_constraint : core::scoring
• CoordinateConstraintCreator_registrator : core
• copy_all_o2star_torsions() : protocols::swa::rna
• copy_bulge_res_and_ribose_torsion() : protocols::swa::rna
• copy_dofs() : core::pose
• copy_dofs_match_atom_names() : core::pose
• copy_hotspot_to_pose() : protocols::protein_interface_design::movers
• copy_internal_coords() : protocols::topology_broker
• copy_residue_coordinates_and_rebuild_missing_atoms() : core::conformation
• copy_residues() : protocols::star
• copy_side_chains() : protocols::abinitio
• copy_stretch() : protocols::protein_interface_design::movers
• copy_torsions_FROM_TO() : protocols::swa::rna
• copy_torsions_to_pose() : protocols::loops::loop_closure::ccd
• CoreDunbrackFilterCOP : protocols::fldsgn::filters
• CoreDunbrackFilterOP : protocols::fldsgn::filters
• Correctly_position_cutpoint_phosphate_torsions() : protocols::swa::rna
• count_atom() : core::scoring::methods
• count_buried_unsat_Hbonds() : protocols::ligand_docking
• count_CBs() : protocols::sic_dock
• count_constraint() : core::scoring::constraints
• count_cutpoints() : protocols::forge::methods
• count_linkers() : protocols::sic_dock
• count_pair_bs() : core::scoring::methods
• CountFromLeftAP : protocols::forge::build
• CountFromLeftCAP : protocols::forge::build
• CountFromLeftCOP : protocols::forge::build
• CountFromLeftOP : protocols::forge::build
• CountPairFunctionCOP : core::scoring::etable::count_pair
• CountPairFunctionOP : core::scoring::etable::count_pair
• CountPairGenericOP : core::scoring::etable::count_pair
• covalent_compliance() : protocols::noesy_assign
• CovalentConnectionReplaceInfoCOP : protocols::toolbox::match_enzdes_util
• CovalentConnectionReplaceInfoOP : protocols::toolbox::match_enzdes_util
• CP_CROSSOVER_3 : core::scoring::etable::count_pair
• CP_CROSSOVER_4 : core::scoring::etable::count_pair
• CP_MULTIPLE_BONDS_OR_PSEUDOBONDS : core::scoring::etable::count_pair
• CP_NO_BONDS : core::scoring::etable::count_pair
• CP_ONE_BOND : core::scoring::etable::count_pair
• CPCrossoverBehavior : core::scoring::etable::count_pair
• CPK_COLOR : protocols::viewer::graphics_states_param
• CPResidueConnectionType : core::scoring::etable::count_pair
• create_acc_orientation_vector() : core::scoring::hbonds
• create_alignment_id_map() : protocols::swa , protocols::swa::rna
• create_cache() : protocols::frag_picker::scores
• create_command_map() : core::pack::task
• create_cpdata_correspondence_for_rotamer() : core::scoring::trie
• create_cpdata_correspondence_for_rotamerset() : core::scoring::trie
• create_don_orientation_vector() : core::scoring::hbonds
• create_euler_rotation() : protocols::swa
• create_extra_output() : protocols::floppy_tail
• create_fragment_set() : protocols::hybridization
• create_full_to_input_res_map() : protocols::swa::rna
• create_match_position_modifier() : protocols::match
• create_minimization_graph() : core::pack
• create_oriented_water_rotamer() : core::pack::rotamer_set
• create_packer_graph() : core::pack
• create_remark_headers_from_cstcache() : protocols::enzdes::enzutil
• create_rna_vall_torsions() : protocols::rna
• create_rotamer_descriptor() : core::scoring::hbonds
• create_scmin_minimizer_map() : core::pack
• create_shuffle_map_recursive_rms() : core::scoring
• create_standard_o2star_pack_task() : protocols::swa::rna
• Create_strand_list() : protocols::swa::rna
• create_subpose() : core::pose
• create_trie() : core::scoring::trie
• CriticalFailure : protocols::loops::loop_mover
• CrossPeakAP : protocols::noesy_assign
• CrossPeakCAP : protocols::noesy_assign
• CrossPeakCOP : protocols::noesy_assign
• CrossPeakInfoAP : protocols::noesy_assign
• CrossPeakInfoCAP : protocols::noesy_assign
• CrossPeakInfoCOP : protocols::noesy_assign
• CrossPeakInfoOP : protocols::noesy_assign
• CrossPeakListAP : protocols::noesy_assign
• CrossPeakListCAP : protocols::noesy_assign
• CrossPeakListCOP : protocols::noesy_assign
• CrossPeakListOP : protocols::noesy_assign
• CrossPeakOP : protocols::noesy_assign
• csa : core::scoring
• csca : core::scoring::rna::chemical_shift
• CSD_TorsionEnergyCOP : core::scoring::methods
• CSD_TorsionEnergyOP : core::scoring::methods
• CSDAtomTypeSetAP : core::chemical
• CSDAtomTypeSetCAP : core::chemical
• CSDAtomTypeSetcontains_atom_type() : core::chemical
• CSDAtomTypeSetCOP : core::chemical
• CSDAtomTypeSetOP : core::chemical
• Csingle : core::chemical::sdf
• CSScoreCOP : protocols::frag_picker::scores
• CSScoreOP : protocols::frag_picker::scores
• cst_res_data : core::scoring
• cst_residue_in_pose() : protocols::toolbox::match_enzdes_util
• cst_respair_data : core::scoring
• CstAction : protocols::enzdes
• CstEnergyContainerCOP : core::scoring::constraints
• CstEnergyContainerOP : core::scoring::constraints
• cstJump : protocols::jumping
• CstMinimizationDataCOP : core::scoring::constraints
• CstMinimizationDataOP : core::scoring::constraints
• cstType : protocols::jumping
• ctabParserTracer() : core::chemical::sdf
• Ctriple : core::chemical::sdf
• CubeKey : core::conformation
• cull_violators() : core::scoring::constraints
• current_batch() : protocols::jd2
• current_job() : protocols::nonlocal
• current_output_filename() : protocols::jd2
• current_output_name() : protocols::jd2
• current_replica() : protocols::jd2
• custom_atom_pair : core::scoring
• CustomAtomPairEnergy_registrator : core
• CustomScoreSelectorCOP : protocols::frag_picker
• CustomScoreSelectorOP : protocols::frag_picker
• cut_point : protocols::loops
• CutBiasClaimerAP : protocols::topology_broker
• CutBiasClaimerCAP : protocols::topology_broker
• CutBiasClaimerCOP : protocols::topology_broker
• CutBiasClaimerOP : protocols::topology_broker
• CutChainMoverCOP : protocols::simple_moves
• CutChainMoverOP : protocols::simple_moves
• CUTPOINT_LOWER() : core::chemical
• cutpoint_probabilities() : protocols::medal
• cutpoint_separation() : protocols::antibody2
• CUTPOINT_UPPER() : core::chemical
• cutpoints_separation() : protocols::antibody2
• CycleMoverCOP : protocols::moves
• CycleMoverOP : protocols::moves
• CyclicMoverCOP : protocols::moves
• CyclicMoverOP : protocols::moves
• cyclize_pose() : protocols::forge::methods
• CYS_C_ALPHA : core::scoring::disulfides
• CYS_C_BETA : core::scoring::disulfides
• CYS_CEN : core::scoring::disulfides
• CYS_S_GAMMA : core::scoring::disulfides