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

- c -

• C : core::chemical::element
• c : core::pack::dunbrack
• C : protocols::forge::build::SegmentInsertConnectionScheme , protocols::sic_dock::scores
• C1_ACETYLAMINO_SUGAR : core::chemical
• C1_AMINO_SUGAR : core::chemical
• C1_BRANCH_POINT : core::chemical
• C1_DEOXY_SUGAR : core::chemical
• C1_METHYLATED_SUGAR : core::chemical
• C1_MODIFIED : core::chemical
• C1_PHOSPHATE : core::chemical
• C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C1_SULFATED_SUGAR : core::chemical
• C1_SULFOAMINO_SUGAR : core::chemical
• C21() : protocols::sic_dock::scores
• C22() : protocols::sic_dock::scores
• C23() : protocols::sic_dock::scores
• C24() : protocols::sic_dock::scores
• C25() : protocols::sic_dock::scores
• C28() : protocols::sic_dock::scores
• C29() : protocols::sic_dock::scores
• C2_ACETYLAMINO_SUGAR : core::chemical
• C2_AMINO_SUGAR : core::chemical
• C2_BRANCH_POINT : core::chemical
• C2_DEOXY_SUGAR : core::chemical
• C2_KETOALDONIC_ACID : core::chemical
• C2_METHYLATED_SUGAR : core::chemical
• C2_MODIFIED : core::chemical
• C2_PHOSPHATE : core::chemical
• C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C2_SULFATED_SUGAR : core::chemical
• C2_SULFOAMINO_SUGAR : core::chemical
• c2n : protocols::rigid
• C30() : protocols::sic_dock::scores
• C3_ACETYLAMINO_SUGAR : core::chemical
• C3_AMINO_SUGAR : core::chemical
• C3_BRANCH_POINT : core::chemical
• C3_DEOXY_SUGAR : core::chemical
• C3_KETOALDONIC_ACID : core::chemical
• C3_METHYLATED_SUGAR : core::chemical
• C3_MODIFIED : core::chemical
• C3_PHOSPHATE : core::chemical
• C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C3_SULFATED_SUGAR : core::chemical
• C3_SULFOAMINO_SUGAR : core::chemical
• C4_ACETYLAMINO_SUGAR : core::chemical
• C4_AMINO_SUGAR : core::chemical
• C4_BRANCH_POINT : core::chemical
• C4_DEOXY_SUGAR : core::chemical
• C4_KETOALDONIC_ACID : core::chemical
• C4_METHYLATED_SUGAR : core::chemical
• C4_MODIFIED : core::chemical
• C4_PHOSPHATE : core::chemical
• C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C4_SULFATED_SUGAR : core::chemical
• C4_SULFOAMINO_SUGAR : core::chemical
• C5_ACETYLAMINO_SUGAR : core::chemical
• C5_AMINO_SUGAR : core::chemical
• C5_BRANCH_POINT : core::chemical
• C5_DEOXY_SUGAR : core::chemical
• C5_KETOALDONIC_ACID : core::chemical
• C5_METHYLATED_SUGAR : core::chemical
• C5_MODIFIED : core::chemical
• C5_PHOSPHATE : core::chemical
• C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C5_SULFATED_SUGAR : core::chemical
• C5_SULFOAMINO_SUGAR : core::chemical
• C6_ACETYLAMINO_SUGAR : core::chemical
• C6_AMINO_SUGAR : core::chemical
• C6_BRANCH_POINT : core::chemical
• C6_DEOXY_SUGAR : core::chemical
• C6_KETOALDONIC_ACID : core::chemical
• C6_METHYLATED_SUGAR : core::chemical
• C6_MODIFIED : core::chemical
• C6_PHOSPHATE : core::chemical
• C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C6_SULFATED_SUGAR : core::chemical
• C6_SULFOAMINO_SUGAR : core::chemical
• C7_ACETYLAMINO_SUGAR : core::chemical
• C7_AMINO_SUGAR : core::chemical
• C7_BRANCH_POINT : core::chemical
• C7_DEOXY_SUGAR : core::chemical
• C7_KETOALDONIC_ACID : core::chemical
• C7_METHYLATED_SUGAR : core::chemical
• C7_MODIFIED : core::chemical
• C7_PHOSPHATE : core::chemical
• C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C7_SULFATED_SUGAR : core::chemical
• C7_SULFOAMINO_SUGAR : core::chemical
• C8_ACETYLAMINO_SUGAR : core::chemical
• C8_AMINO_SUGAR : core::chemical
• C8_BRANCH_POINT : core::chemical
• C8_DEOXY_SUGAR : core::chemical
• C8_KETOALDONIC_ACID : core::chemical
• C8_METHYLATED_SUGAR : core::chemical
• C8_MODIFIED : core::chemical
• C8_PHOSPHATE : core::chemical
• C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C8_SULFATED_SUGAR : core::chemical
• C8_SULFOAMINO_SUGAR : core::chemical
• C9_ACETYLAMINO_SUGAR : core::chemical
• C9_AMINO_SUGAR : core::chemical
• C9_BRANCH_POINT : core::chemical
• C9_DEOXY_SUGAR : core::chemical
• C9_METHYLATED_SUGAR : core::chemical
• C9_MODIFIED : core::chemical
• C9_PHOSPHATE : core::chemical
• C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR : core::chemical
• C9_SULFATED_SUGAR : core::chemical
• C9_SULFOAMINO_SUGAR : core::chemical
• C_ALA : protocols::match
• c_array_mult() : core::scoring::fiber_diffraction
• C_CAR : protocols::match
• C_METHYLAMIDATION : core::chemical
• C_METHYLATED_SUGAR : core::chemical
• c_mult_ip() : core::scoring::fiber_diffraction
• C_pi_sp2 : core::chemical::orbitals
• Ca : core::chemical::element
• CA : protocols::frag_picker , protocols::sic_dock::scores
• Ca_coord() : protocols::simple_moves
• Ca_coords() : protocols::protein_interface_design::filters , protocols::simple_moves
• CA_gdtmm() : core::scoring
• CA_gdttm() : core::scoring
• CA_maxsub() : core::scoring
• CA_maxsub_by_subset() : core::scoring
• CA_rmsd() : core::scoring
• CA_rmsd_symmetric() : core::scoring
• CA_Sscore() : protocols::mpi_refinement
• 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
• CachingScoringMethodCOP : protocols::frag_picker::scores
• CachingScoringMethodOP : protocols::frag_picker::scores
• cal_dis_angle_to_find_sheet() : protocols::features::strand_assembly
• cal_min_avg_dis_between_sheets_by_cen_res() : protocols::features::strand_assembly
• cal_min_avg_dis_between_two_sheets_by_cen_res() : protocols::features::strand_assembly
• cal_min_dis_between_sheets_by_all_res() : protocols::features::strand_assembly
• cal_min_dis_between_two_sheets_by_all_res() : protocols::features::strand_assembly
• cal_num_of_sheets_that_surround_this_sheet() : protocols::features::strand_assembly
• cal_shortest_dis_between_facing_aro_in_sw() : protocols::features::strand_assembly
• calc_all_averages() : protocols::unfolded_state_energy_calculator
• calc_all_dist() : protocols::make_rot_lib
• calc_angle_rmsd() : protocols::membrane
• calc_approx_loop_length() : protocols::denovo_design::connection
• calc_atom_masks() : core::scoring
• calc_CA_Irmsd() : protocols::docking
• calc_centroids() : protocols::make_rot_lib
• calc_delta_sasa() : protocols::fldsgn::topology
• calc_dist() : protocols::make_rot_lib
• calc_fit_R() : protocols::toolbox
• calc_Fnat() : protocols::docking
• calc_Fnonnat() : protocols::docking
• calc_helix_axis() : protocols::membrane
• calc_helix_tilt_angle() : protocols::membrane
• calc_interacting_vector() : core::select::util
• calc_interaction_energy() : protocols::docking
• calc_interface_vector() : core::select::util
• calc_intf_score() : protocols::docking
• calc_Irmsd() : protocols::docking
• calc_Lrmsd() : protocols::docking
• calc_P1rmsd() : protocols::docking
• calc_P2rmsd() : protocols::docking
• calc_pareto_front() : protocols::design_opt , protocols::matdes
• calc_pareto_front_nbrs() : protocols::design_opt , protocols::matdes
• calc_per_atom_sasa() : core::scoring
• calc_per_atom_sasa_sc() : core::scoring
• calc_per_res_hydrophobic_sasa() : core::scoring
• calc_per_residue_scores() : protocols::sparta
• calc_res_contact() : protocols::docking
• CALC_RMS : core::pose::full_model_info
• calc_rotamer_clusters() : protocols::make_rot_lib
• calc_rsd_sasa() : protocols::forge::methods
• calc_std_dev() : protocols::make_rot_lib
• 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
• CalcInterNeighborGroupCOP : protocols::toolbox
• CalcInterNeighborGroupOP : protocols::toolbox
• calculate_chi2_free() : core::scoring::fiber_diffraction
• calculate_chi_k() : core::scoring::fiber_diffraction
• calculate_derivatives_gpu() : core::scoring::fiber_diffraction
• calculate_dihedral_distance() : protocols::antibody::clusters
• calculate_dihedral_w_4_resnums() : protocols::features::strand_assembly
• calculate_I_of_E() : core::scoring::fiber_diffraction
• calculate_intensity_gpu() : core::scoring::fiber_diffraction
• calculate_intra_res_hbonds() : core::scoring::hbonds
• calculate_inverting_virtuals() : core::conformation::symmetry
• calculate_rigid_matrix() : core::chemical
• calculate_statistics() : protocols::ncbb
• CalculatorFilterCOP : protocols::filters
• CalculatorFilterOP : protocols::filters
• calDist() : protocols::pockets
• 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::antibody
• CAN_CONTROL : protocols::environment::claims
• 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_AA : core::chemical
• canonical_atom_count() : core::pose
• CANONICAL_NUCLEIC : core::chemical
• canonical_residue_count() : core::pose
• canonical_sampling_main() : protocols::canonical_sampling
• CanonicalSamplingMoverCOP : protocols::canonical_sampling
• CanonicalSamplingMoverOP : protocols::canonical_sampling
• CARBOHYDRATE : core::chemical
• CarbohydrateInfoCOP : core::chemical::carbohydrates
• CarbohydrateInfoOP : core::chemical::carbohydrates
• CarbonHBondEnergyCreator_registrator : core::init
• CarbonHBondPotentialCOP : core::scoring::carbon_hbonds
• CarbonHBondPotentialOP : core::scoring::carbon_hbonds
• CARBOXYLATION : core::chemical
• 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::init
• CartesianBondedEnergyOP : core::scoring::methods
• CartesianHybridizeCOP : protocols::hybridization
• CartesianHybridizeOP : protocols::hybridization
• CartesianMDCOP : protocols::md
• CartesianMDOP : protocols::md
• CartesianMinimizerCOP : core::optimization
• CartesianMinimizerMapCOP : core::optimization
• CartesianMinimizerMapOP : core::optimization
• CartesianMinimizerOP : core::optimization
• CartesianNormalModeMoverCOP : protocols::normalmode
• CartesianNormalModeMoverOP : protocols::normalmode
• CartesianSamplerCOP : protocols::hybridization
• CartesianSamplerOP : protocols::hybridization
• CartGridIntOP : protocols::ligand_docking
• 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
• CAVEAT : core::io::pdb
• cavity_distance_constraint() : core::scoring::packstat
• CB : protocols::frag_picker , protocols::sic_dock::scores
• 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_map() : protocols::sic_dock
• cb_weights_from_pose() : protocols::sic_dock
• cbeta : core::scoring
• cbeta_smooth : core::scoring
• cbeta_vector() : core::select::util
• CBlocal() : protocols::sic_dock::scores
• CBScore_dist_score() : protocols::sic_dock
• CBScoreCOP : protocols::sic_dock
• CBScoreOP : protocols::sic_dock
• CBSG_Dihedral_FuncOP : core::scoring::disulfides
• CCD() : protocols::loops::loop_mover
• ccd_close_loops() : protocols::loops
• CCDEndsGraftMoverCOP : protocols::grafting
• CCDEndsGraftMoverOP : protocols::grafting
• 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_atomwise
• Cd : core::chemical::element
• CD() : protocols::sic_dock::scores
• cd_1b : core::scoring::methods
• cd_2b : core::scoring::methods
• cd_lr_2b : core::scoring::methods
• CDFr : protocols::fldsgn::topology
• cdr_CN_anchor_distance() : protocols::antibody
• cdr_end : protocols::antibody
• cdr_energy() : protocols::antibody
• CDR_H3_cter_filter() : protocols::antibody
• CDR_H3_filter_legacy_code_with_old_rule() : protocols::antibody
• cdr_has_res_constraints() : protocols::antibody::constraints
• cdr_region : protocols::antibody
• cdr_start : protocols::antibody
• CDRClusterCOP : protocols::antibody::clusters
• CDRClusterEnum : protocols::antibody::clusters
• CDRClusterEnum_start : protocols::antibody::clusters
• CDRClusterEnum_stop : protocols::antibody::clusters
• CDRClusterEnum_total : protocols::antibody::clusters
• CDRClusterEnumManagerCOP : protocols::antibody::clusters
• CDRClusterEnumManagerOP : protocols::antibody::clusters
• CDRClusterFeaturesCOP : protocols::antibody::clusters
• CDRClusterFeaturesOP : protocols::antibody::clusters
• CDRClusterMatcherCOP : protocols::antibody::clusters
• CDRClusterMatcherOP : protocols::antibody::clusters
• CDRClusterOP : protocols::antibody::clusters
• CDRClusterSetCOP : protocols::antibody::clusters
• CDRClusterSetOP : protocols::antibody::clusters
• CDRDBPoseSet : protocols::antibody
• CDRDBSequenceSet : protocols::antibody
• CDRDefinitionEnum : protocols::antibody
• CDRDefinitionEnum_start : protocols::antibody
• CDRDefinitionEnum_total : protocols::antibody
• CDRDihedralConstraintMoverCOP : protocols::antibody::constraints
• CDRDihedralConstraintMoverOP : protocols::antibody::constraints
• CDRGraftDesignOptionsCOP : protocols::antibody::design
• CDRGraftDesignOptionsOP : protocols::antibody::design
• CDRGraftDesignOptionsParserCOP : protocols::antibody::design
• CDRGraftDesignOptionsParserOP : protocols::antibody::design
• CDRH3ModelerCOP : protocols::antibody_legacy
• CDRH3ModelerOP : protocols::antibody_legacy
• CDRLandmarkEnum : protocols::antibody
• CDRLandmarkEnum_total : protocols::antibody
• CDRNameEnum : protocols::antibody
• CDRNameEnum_proto_start : protocols::antibody
• CDRNameEnum_proto_total : protocols::antibody
• CDRNameEnum_start : protocols::antibody
• CDRNameEnum_total : protocols::antibody
• CDRSeqDesignOptionsCOP : protocols::antibody::design
• CDRSeqDesignOptionsOP : protocols::antibody::design
• CDRSeqDesignOptionsParserCOP : protocols::antibody::design
• CDRSeqDesignOptionsParserOP : protocols::antibody::design
• CDRSetOptionsCOP : protocols::antibody
• CDRSetOptionsOP : protocols::antibody
• CDRSetOptionsParserCOP : protocols::antibody
• CDRSetOptionsParserOP : protocols::antibody
• CDRsMinPackMinCOP : protocols::antibody
• CDRsMinPackMinOP : protocols::antibody
• Ce : core::chemical::element
• 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_motif_degree : core::scoring
• cen_pair_motifs : core::scoring
• cen_pair_smooth : core::scoring
• cen_rot_cbeta : core::scoring
• cen_rot_dun : core::scoring
• cen_rot_env : core::scoring
• cen_rot_pair : core::scoring
• cen_rot_pair_ang : core::scoring
• cen_rot_pair_dih : core::scoring
• CenHBEnergyCreator_registrator : core::init
• CenHBPotentialCOP : core::scoring
• CenHBPotentialOP : core::scoring
• CenListInfoOP : core::scoring
• cenpack : core::scoring
• cenpack_smooth : core::scoring
• CenPairEnergyCreator_registrator : core::init
• CenPairMotifDegreeEnergyCreator_registrator : core::init
• CenPairMotifEnergyCreator_registrator : core::init
• CenRotDunEnergyCreator_registrator : core::init
• CenRotEnvEnergyCreator_registrator : core::init
• CenRotEnvPairPotentialCOP : core::scoring
• CenRotEnvPairPotentialOP : core::scoring
• CenrotLibraryCOP : core::pack::dunbrack::cenrot
• CenrotLibraryOP : core::pack::dunbrack::cenrot
• CenRotPairEnergyCreator_registrator : core::init
• CenrotRotamerLibrarySpecificationCOP : core::chemical::rotamers
• CenrotRotamerLibrarySpecificationCreator_registrator : core::init
• CenrotRotamerLibrarySpecificationOP : core::chemical::rotamers
• center : core::conformation::membrane
• center_of_geom() : protocols::sic_dock
• center_of_mass() : core::pose , protocols::geometry
• CENTROID : core::chemical
• centroid_dist() : protocols::toolbox::sample_around
• CENTROID_DISTANCE : protocols::stepwise::screener
• centroid_disulfide_energy : core::scoring::methods
• centroid_neighbor_graph : core::scoring
• centroid_pair_by_jump() : protocols::geometry
• centroid_pose_from_pdb() : core::import_pose
• centroid_relax : protocols::antibody::design
• CENTROID_ROT : core::chemical
• centroid_scatter() : core::scoring::fiber_diffraction
• CENTROID_WITH_HA : core::chemical
• CENTROID_WTS : core::scoring
• CentroidDistanceScreenerCOP : protocols::stepwise::screener
• CentroidDistanceScreenerOP : protocols::stepwise::screener
• CentroidDisulfideEnergyContainerAP : core::scoring::disulfides
• CentroidDisulfideEnergyContainerCAP : core::scoring::disulfides
• CentroidDisulfideEnergyContainerCOP : core::scoring::disulfides
• CentroidDisulfideEnergyContainerOP : core::scoring::disulfides
• CentroidDisulfideEnergyCOP : core::scoring::disulfides
• CentroidDisulfideEnergyCreator_registrator : core::init
• 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
• CentroidRotNumVec : protocols::make_rot_lib
• CentroidRotNumVecVec : protocols::make_rot_lib
• centroids_by_jump() : protocols::geometry
• centroids_by_jump_int() : protocols::geometry
• CentroidScatterOP : core::scoring::fiber_diffraction
• Cf : core::chemical::element
• CFr : protocols::fldsgn::topology
• CG() : protocols::sic_dock::scores
• 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_com() : protocols::membrane
• chain_end_res() : core::pose
• chain_gws_string() : core::io::carbohydrates
• chain_tm_com() : protocols::membrane
• ChainAtoms : core::io
• 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::init
• ChainDirection : protocols::loops::loop_closure::ccd
• chainID : protocols::loops
• ChainIsCreator_registrator : core::init
• ChainIsntCreator_registrator : core::init
• ChainIsntOP : core::pack::task::operation
• ChainIsOP : core::pack::task::operation
• ChainSelectorCOP : core::select::residue_selector
• ChainSelectorOP : core::select::residue_selector
• ChainSplitMoverCOP : protocols::simple_moves
• ChainSplitMoverOP : protocols::simple_moves
• change_cys_state() : core::conformation
• change_jump_to_this_residue_into_chemical_edge() : core::pose
• change_sheet_id_if_possible() : protocols::features::strand_assembly
• ChangeAndResetFoldTreeMoverCOP : protocols::simple_moves
• ChangeAndResetFoldTreeMoverOP : protocols::simple_moves
• ChangeFoldTreeMoverCOP : protocols::moves
• ChangeFoldTreeMoverOP : protocols::moves
• char_to_int() : core::io::carbohydrates
• char_valid_as_torsion_bin() : core::conformation
• character_is_USA_letter() : core::pose
• Charge : core
• ChargeChargeFeaturesCOP : protocols::features
• ChargeChargeFeaturesOP : protocols::features
• CHARGED : core::chemical
• chco : core::scoring::rna::chemical_shift
• check_all_ligand_atoms() : protocols::ligand_docking::ligand_options
• check_all_residues_sampled() : core::pose::full_model_info
• check_and_correct_sister_atom_based_on_chirality() : core::io::pose_from_sfr
• check_and_correct_sister_atom_based_on_outgroup() : core::io::pose_from_sfr
• check_and_correct_sister_atoms() : core::io::pose_from_sfr
• check_base_pair() : protocols::farna
• check_binary_chars() : core::io::serialization
• check_binary_unsigned_int() : core::io::serialization
• check_can_append() : protocols::stepwise::legacy::modeler::rna
• check_can_prepend() : protocols::stepwise::legacy::modeler::rna
• check_canonicalness_of_LR() : protocols::features::strand_assembly
• check_canonicalness_of_PA() : protocols::features::strand_assembly
• check_canonicalness_of_parallel_EE() : protocols::features::strand_assembly
• check_cb() : protocols::antibody::design
• check_deprecated_flags() : core::init
• check_extra_minimize_res_are_input() : protocols::stepwise::setup
• check_fix_aho_cdr_numbering() : protocols::antibody
• check_for_connections_for_all_submotif_residues() : protocols::stepwise::monte_carlo::mover
• check_for_input_domain() : protocols::stepwise::modeler
• check_for_messed_up_structure() : protocols::stepwise::modeler::rna
• check_full_model_info_OK() : core::pose::full_model_info
• check_good_neighbor() : core::conformation
• check_hbonds : core::optimization::symmetry
• check_heading_direction() : protocols::features::strand_assembly
• check_helix_existence() : protocols::features::strand_assembly
• check_if_applicable() : core::chemical::carbohydrates
• check_if_pose_renumbered_for_clusters() : protocols::antibody::clusters
• check_if_proton_chi_atom() : protocols::simple_moves , protocols::stepwise::modeler::polar_hydrogens
• check_in_base_pair_list() : protocols::farna
• check_insert_ss_and_abego() : protocols::denovo_design::connection
• check_instantiated_O2Prime_hydrogen() : protocols::stepwise::modeler::rna
• check_internal_hbonds() : protocols::fldsgn::topology
• check_is_working_res() : protocols::stepwise::modeler::rna
• check_jump_to_next_residue_in_chain() : protocols::stepwise::modeler
• check_jump_to_previous_residue_in_chain() : protocols::stepwise::modeler
• check_kink_helix() : protocols::fldsgn::topology
• check_LR() : protocols::features::strand_assembly
• check_move_map_against_working_parameters() : protocols::stepwise::modeler::movemap
• check_neighbor_ligand_atom() : protocols::ligand_docking::ligand_options
• check_o2prime_contact() : protocols::stepwise::modeler::packer
• check_order() : protocols::denovo_design::connection
• check_PA() : protocols::features::strand_assembly
• check_phosphate_contacts_donor() : protocols::stepwise::modeler::rna::phosphate
• 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_sample_sugar_in_full_model_info() : core::pose::full_model_info
• check_score() : protocols::ligand_docking
• check_score_components : core::optimization::symmetry
• check_score_components_verbose : core::optimization::symmetry
• check_score_function_sanity() : core::init
• check_scorefxn_has_constraint_terms_if_pose_has_constraints() : protocols::stepwise::modeler
• check_scores_from_parts() : protocols::stepwise::modeler
• check_strand_too_closeness() : protocols::features::strand_assembly
• check_surface_area_leerichards_deriv() : core::scoring::packstat
• check_sw_by_dis() : protocols::features::strand_assembly
• check_validity_and_get_working_res() : protocols::stepwise::modeler::rna
• check_vector() : protocols::membrane
• check_whether_hairpin_connects_short_strand() : protocols::features::strand_assembly
• check_whether_same_direction_strands_connect_two_sheets_or_a_loop() : protocols::features::strand_assembly
• check_whether_sheets_are_connected_with_near_bb_atoms() : protocols::features::strand_assembly
• check_whether_strand_i_is_in_sheet() : protocols::features::strand_assembly
• check_whether_sw_by_sh_id_still_alive() : protocols::features::strand_assembly
• check_whether_sw_is_not_connected_with_continuous_atoms() : protocols::features::strand_assembly
• check_whether_this_pdb_should_be_excluded() : protocols::features::strand_assembly
• check_whether_this_sheet_is_too_short() : protocols::features::strand_assembly
• check_working_res() : protocols::stepwise::setup
• checkpoint_cleanup() : protocols::dna
• checkpoint_with_interval() : protocols::checkpoint
• CheckPointerCOP : protocols::checkpoint
• CheckPointerOP : protocols::checkpoint
• ChemicalShiftAnisotropyCOP : core::scoring
• ChemicalShiftAnisotropyEnergyCreator_registrator : core::init
• ChemicalShiftAnisotropyEnergyOP : core::scoring::methods
• ChemicalShiftAnisotropyOP : core::scoring
• ChemicalShiftSequenceCOP : core::sequence
• ChemicalShiftSequenceOP : core::sequence
• CHI : core::chemical::rna , core::id , core::scoring::dna
• CHI1 : core::scoring
• chi1_torsion_atom() : core::chemical::rna
• chi1_torsion_atom_index() : core::chemical::rna
• CHI2 : core::scoring
• chi2_torsion_atom_index() : core::scoring::hackaro
• CHI3 : core::scoring
• CHI4 : core::scoring
• CHI_ATOM : core::chemical
• chi_continuation() : core::conformation
• chi_interruption() : core::conformation
• CHIEnergyFunctionCOP : core::scoring::carbohydrates
• CHIEnergyFunctionOP : core::scoring::carbohydrates
• CHIMERA_SEGMENT : protocols::sewing
• chiral : protocols::sic_dock::scores
• chiral1() : protocols::sic_dock::scores
• chiral2() : protocols::sic_dock::scores
• chiral3() : protocols::sic_dock::scores
• chiral4() : protocols::sic_dock::scores
• 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
• ChiState : core::chemical::rna
• ChiStrategy : protocols::match::upstream
• ChiVector : core::pack::dunbrack
• choose_effective_sequence_separation() : core::scoring::constraints
• choose_hbond_parameter_set() : protocols::toolbox::pose_metric_calculators
• choose_random_if_unspecified_nucleotide() : protocols::stepwise::modeler::rna
• chop_fragments() : core::fragment
• chothia : core::scoring::sasa
• Chothia : protocols::antibody
• Chothia_Scheme : protocols::antibody
• chr_chains() : core::chemical , core::conformation::symmetry
• chrg : core::scoring::rna::chemical_shift
• chunk_probabilities() : protocols::medal
• ChunkCOP : protocols::nonlocal
• ChunkOP : protocols::nonlocal
• chunks_by_CA_CA_distance() : protocols::nonlocal
• ChunkSetCOP : protocols::farna::libraries
• ChunkSetOP : protocols::farna::libraries
• ChunkTrialMoverCOP : protocols::hybridization
• ChunkTrialMoverOP : protocols::hybridization
• ci_1b : core::scoring::methods
• ci_2b : core::scoring::methods
• ci_lr_2b : core::scoring::methods
• CIF_file : core::import_pose
• CifFileOP : core::chemical::mmCIF
• CifParserOP : core::chemical::mmCIF
• CircleIter : core::scoring::packstat
• Circles : core::scoring::packstat
• CircularGeneral1D_FuncCOP : core::scoring::func
• CircularGeneral1D_FuncOP : core::scoring::func
• CircularHarmonicFuncCOP : core::scoring::func
• CircularHarmonicFuncOP : core::scoring::func
• CircularPermutation_AP : protocols::fldsgn
• CircularPermutation_CAP : protocols::fldsgn
• CircularPermutation_COP : protocols::fldsgn
• CircularPermutation_OP : protocols::fldsgn
• CircularPowerFuncCOP : core::scoring::func
• CircularPowerFuncOP : core::scoring::func
• CircularSigmoidalFuncCOP : core::scoring::func
• CircularSigmoidalFuncOP : core::scoring::func
• CircularSplineFuncCOP : core::scoring::func
• CircularSplineFuncOP : core::scoring::func
• CIS : core::chemical::rna
• cis_omega_torsion_bin() : core::conformation
• CISPEP : core::io::pdb
• Cl : core::chemical::element
• ClaimerMessageAP : protocols::topology_broker
• ClaimerMessageCAP : protocols::topology_broker
• ClaimerMessageCOP : protocols::topology_broker
• ClaimerMessageOP : protocols::topology_broker
• ClaimStrengthAP : protocols::environment::claims
• ClaimStrengthCAP : protocols::environment::claims
• ClaimStrengthCOP : protocols::environment::claims
• ClaimStrengthOP : protocols::environment::claims
• clash_coords : protocols::sic_dock::scores
• ClashBasedRepackShellSelectorCOP : core::pack::task::residue_selector
• ClashBasedRepackShellSelectorOP : core::pack::task::residue_selector
• ClashCheckFilterCOP : protocols::matdes
• ClashCheckFilterOP : protocols::matdes
• ClashScorerCOP : protocols::sewing::scoring
• ClashScorerOP : protocols::sewing::scoring
• 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() : core::pose::rna
• classify_base_pairs_lores() : protocols::farna
• clean_for_storage() : protocols::denovo_design::components
• clean_from_storage() : protocols::denovo_design::components
• cleanup() : protocols::stepwise::setup
• clear_conformation_viewers() : protocols::viewer
• CLEAR_IF_CACHING_FRAGMENTS : protocols::forge::components::VLB_VallMemoryUsage
• clear_rna_scoring_info() : core::scoring::rna
• clear_rna_secstruct_info() : protocols::farna::secstruct
• ClearCompositionConstraintsMoverCOP : protocols::aa_composition
• ClearCompositionConstraintsMoverOP : protocols::aa_composition
• clearPoseExtraScore() : core::pose
• clearPoseExtraScores() : core::pose
• ClientMoverAP : protocols::environment
• ClientMoverCAP : protocols::environment
• ClientMoverCOP : protocols::environment
• ClientMoverOP : protocols::environment
• close_chainbreaks() : protocols::jumping
• close_to_dna() : protocols::dna
• closed_range() : protocols::forge::methods
• CloseOneCDRLoopCOP : protocols::antibody
• CloseOneCDRLoopOP : protocols::antibody
• CloseOneMoverCOP : protocols::antibody_legacy
• CloseOneMoverOP : protocols::antibody_legacy
• Closest : protocols::indexed_structure_store::filters
• closest_larger_peptide_vertex() : protocols::forge::methods
• closest_smaller_peptide_vertex() : protocols::forge::methods
• ClosureProblemCOP : protocols::kinematic_closure
• ClosureProblemOP : protocols::kinematic_closure
• ClosureSolutionCOP : protocols::kinematic_closure
• ClosureSolutionOP : protocols::kinematic_closure
• 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 : core::chemical::element
• cm_main() : protocols::comparative_modeling
• CMCT : core::scoring::rna::data
• cmp() : protocols::loophash
• cmp_pair_by_first_vec_val() : protocols::design_opt , protocols::matdes
• cmp_pair_by_second() : protocols::design_opt , protocols::matdes
• cmp_pair_vec_by_first_vec_val() : protocols::design_opt , protocols::matdes
• cmp_particles() : core::optimization
• Cn : core::chemical::element
• Co : core::chemical::element
• co : core::scoring
• COARSE : core::chemical
• 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
• CoarseRNA_LoopCloserOP : protocols::coarse_rna
• coil : protocols::loops::loop_closure::ccd
• collect_dofs() : protocols::environment
• ColorMode : protocols::viewer::graphics_states_param
• com() : protocols::membrane
• com_calc() : protocols::environment
• COMB : protocols::stepwise::sampler
• combinable() : core::scoring::constraints
• combine_and_trim() : protocols::nonlocal
• combine_constraints() : core::scoring::constraints
• combine_loops() : protocols::medal
• combine_movemaps_post_insertion() : protocols::grafting
• 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
• CombinePoseMoverCOP : protocols::simple_moves
• CombinePoseMoverOP : protocols::simple_moves
• comma_separated_partner_chains() : protocols::docking
• comma_strings_to_map() : core::conformation::symmetry
• comma_strings_to_pair_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
• common_simple_types() : core::select::residue_selector
• compact_enum_set() : core::chemical::gasteiger
• compare() : protocols::fldsgn::topology
• compare_atom_coordinates() : core::pose
• compare_binary_protein_silent_struct() : core::pose
• compare_by_abs() : core::scoring
• compare_insert_ss_and_abego() : protocols::denovo_design::connection
• compare_mingraph_and_energy_graph() : core::pack
• compare_motif2scaffold_data_by_scaffold_low2high() : protocols::motif_grafting::movers
• compare_RNA_char() : protocols::farna
• compare_RNA_secstruct() : protocols::farna
• compare_sequence_claim_priority() : protocols::topology_broker
• 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
• complex_ring_detection() : core::chemical
• complex_type_name_for_residue_selector() : core::select::residue_selector
• COMPND : core::io::pdb
• CompositeScoringSchemeOP : core::sequence
• CompositeSegment : protocols::rbsegment_relax
• CompositeSequenceCOP : core::sequence
• CompositeSequenceCreator_registrator : core::init
• CompositeSequenceOP : core::sequence
• CompositionMoverCOP : protocols::moves
• CompositionMoverOP : protocols::moves
• CompoundFilterCOP : protocols::filters
• CompoundFilterOP : protocols::filters
• compute_and_store_pose_waters() : core::scoring::lkball
• compute_atom_packing_scores() : core::scoring::packstat
• compute_avge_scores() : protocols::sasa_scores
• compute_bb_centroid() : core::scoring
• compute_bb_radius() : core::scoring
• compute_bulges() : protocols::fldsgn::topology
• compute_cav_ball_clusters() : core::scoring::packstat
• compute_cav_ball_neighbor_count() : core::scoring::packstat
• compute_cav_ball_volumes() : core::scoring::packstat
• compute_center_of_mass() : protocols::forge::remodel
• compute_coefficients3() : core::scoring::electron_density::SplineInterp
• compute_coefficients4() : core::scoring::electron_density::SplineInterp
• compute_dec15_score() : core::scoring::packing
• compute_embeddings_by_chain() : protocols::membrane
• 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_max_strand() : protocols::fldsgn::filters
• compute_packing_score() : core::scoring::packstat
• compute_packing_score_leerichards() : core::scoring::packstat
• compute_paired_residues() : protocols::fldsgn::filters
• compute_per_residue_coverage() : core::fragment
• compute_per_residue_probabilities() : protocols::star
• compute_rdf_tracer() : protocols::ligand_docking
• 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_single_direction_deviation() : protocols::loops::loop_closure::ccd
• compute_smooth_nb_deriv() : core::scoring::packing
• compute_ss_regions() : protocols::loops
• compute_structure_based_embedding() : protocols::membrane
• compute_surface_area_leerichards() : core::scoring::packstat
• compute_surface_area_leerichards_deriv() : core::scoring::packstat
• compute_surrounding_sasa() : core::scoring::packstat
• compute_total_paired_residues() : protocols::fldsgn::filters
• compute_unique_chains() : core::pose
• ComputeLigandRDFCOP : protocols::ligand_docking
• ComputeLigandRDFOP : protocols::ligand_docking
• CoMTrackerCMCOP : protocols::environment
• CoMTrackerCMOP : protocols::environment
• ConcurrencyTestCOP : protocols::features::helixAssembly
• ConcurrencyTestOP : protocols::features::helixAssembly
• CONECT : core::io::pdb
• conf2pdb_chain() : core::pose
• conf2pdb_chain_default_map() : core::pose
• configure_rmc() : protocols::star
• ConformationAP : core::conformation
• ConformationCAP : core::conformation
• ConformationCOP : core::conformation
• ConformationKinWriterCOP : core::conformation
• ConformationKinWriterOP : core::conformation
• ConformationOP : core::conformation
• ConformationViewerOP : protocols::viewer
• ConformerSwitchMoverCOP : protocols::docking
• ConformerSwitchMoverOP : protocols::docking
• conj_map_times() : core::scoring::electron_density
• ConjugableBond : core::chemical
• connect_from() : protocols::protein_interface_design::movers
• connect_to() : protocols::protein_interface_design::movers
• connected_mainchain_atomids() : protocols::backrub
• connection_indices() : core::scoring::mm
• ConnectionAP : protocols::denovo_design::connection
• ConnectionCAP : protocols::denovo_design::connection
• ConnectionCOP : protocols::denovo_design::connection
• ConnectionOP : protocols::denovo_design::connection
• 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
• ConsensusLoopDesignOperationCOP : protocols::denovo_design::task_operations
• ConsensusLoopDesignOperationOP : protocols::denovo_design::task_operations
• ConsensusSequenceTable : protocols::denovo_design::task_operations
• ConservativeDesignOperationCOP : protocols::toolbox::task_operations
• ConservativeDesignOperationOP : protocols::toolbox::task_operations
• ConservedPosMutationFilterCOP : protocols::simple_filters
• ConservedPosMutationFilterOP : protocols::simple_filters
• const_full_model_info() : core::pose::full_model_info
• const_vdw_cached_rep_screen_info_from_pose() : protocols::stepwise::modeler::rna::checker
• ConstAbinitioMoverWeightAP : protocols::topology_broker::weights
• ConstAbinitioMoverWeightCAP : protocols::topology_broker::weights
• ConstAbinitioMoverWeightCOP : protocols::topology_broker::weights
• ConstAbinitioMoverWeightOP : protocols::topology_broker::weights
• constant_constraint : core::scoring
• ConstantConstraintCOP : core::scoring::constraints
• ConstantConstraintOP : core::scoring::constraints
• ConstantFuncOP : core::scoring::func
• ConstantLengthFragSetCOP : core::fragment
• ConstantLengthFragSetOP : core::fragment
• constrain_ligand_torsions() : protocols::ligand_docking
• constrain_pose_res_to_invrots() : protocols::toolbox::match_enzdes_util
• constrain_residue() : protocols::mpi_refinement
• constrain_ring_atoms() : core::pose::ncbb
• constrained_optimization_weight_func : protocols::optimize_weights
• constraint_set_slice() : protocols::stepwise::modeler
• 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
• ConstraintFragmentSamplerOP : protocols::abinitio
• ConstraintGeneratorAP : protocols::moves
• ConstraintGeneratorCAP : protocols::moves
• ConstraintGeneratorCOP : protocols::moves
• ConstraintGeneratorOP : protocols::moves
• ConstraintGraphCOP : core::scoring::constraints
• ConstraintGraphOP : core::scoring::constraints
• ConstrainToIdealMoverCOP : protocols::simple_moves
• ConstrainToIdealMoverOP : protocols::simple_moves
• ConstraintOP : core::scoring::constraints
• ConstraintOPs : core::scoring::constraints , protocols::flxbb
• ConstraintPreparerCOP : protocols::abinitio::abscript
• ConstraintPreparerOP : protocols::abinitio::abscript
• 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::init
• ConstraintsEnergyOP : core::scoring::constraints
• ConstraintSetCOP : core::scoring::constraints
• ConstraintSetMoverCOP : protocols::simple_moves
• ConstraintSetMoverOP : protocols::simple_moves
• ConstraintSetOP : core::scoring::constraints
• ConstraintSetScoreCOP : protocols::sic_dock
• ConstraintSetScoreOP : protocols::sic_dock
• ConstraintsOP : core::scoring::constraints
• construct_dummy_pose() : protocols::denovo_design
• construct_poly_ala_pose() : protocols::denovo_design , protocols::toolbox::pose_manipulation
• construct_poly_d_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::init
• ContactPartnerAP : protocols::contact_map
• CONTACTS : core::conformation::symmetry
• ContactType : protocols::frag_picker
• contain_residue_at_seq_num() : protocols::stepwise::modeler::rna
• Contain_seq_num() : core::scoring::rna::chemical_shift
• contains() : protocols::sparta
• Contains() : protocols::toolbox
• contains_protein() : protocols::stepwise::modeler::protein
• contains_stageid() : protocols::abinitio
• ContextDependentGeometricSolEnergyCreator_registrator : core::init
• 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::init
• ContextIndependentLRTwoBodyEnergyCOP : core::scoring::methods
• ContextIndependentLRTwoBodyEnergyOP : core::scoring::methods
• ContextIndependentOneBodyEnergyCOP : core::scoring::methods
• ContextIndependentOneBodyEnergyOP : core::scoring::methods
• ContextIndependentTwoBodyEnergyCOP : core::scoring::methods
• ContextIndependentTwoBodyEnergyOP : core::scoring::methods
• ContingentAcceptMoverCOP : protocols::simple_moves
• ContingentAcceptMoverOP : protocols::simple_moves
• 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
• ControlStrength : protocols::environment::claims
• ControlStrengths : protocols::environment::claims
• convert_acgu_to_1234() : core::chemical::rna
• convert_atom_name() : core::io::pose_from_sfr
• convert_based_on_match_type() : protocols::farna
• convert_cartesian_to_grid() : protocols::pockets
• convert_cartesian_to_spherical_coor_triplet() : protocols::pockets
• convert_from_std_map() : core::pose
• convert_grid_to_cartesian() : protocols::pockets
• 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::stepwise::modeler::rna
• convert_res_name() : core::io::pose_from_sfr
• convert_residue_names_into_linkage_map_key() : core::chemical::carbohydrates
• convert_residuetype_to_light_graph() : core::chemical
• convert_spherical_coor_triplet_to_cartesian() : protocols::pockets
• convert_sugar_modeling_to_residue_alternative_set() : protocols::stepwise::modeler::rna::sugar
• convert_to_BondName() : core::chemical
• convert_to_ResidueType() : core::chemical::sdf
• convert_to_ResidueTypes() : core::chemical::sdf
• convert_to_vector1() : protocols::stepwise::legacy::modeler::protein
• convert_to_working_res() : protocols::stepwise::legacy::modeler::protein
• ConvertToInterpolationCoefficients() : core::scoring::electron_density::SplineInterp
• convolute_maps() : core::scoring::electron_density
• coordinate_constrain_selection() : protocols::relax
• coordinate_constraint : core::scoring
• CoordinateConstraintCreator_registrator : core::init
• CoordinateConstraintGeneratorAP : protocols::denovo_design::constraints
• CoordinateConstraintGeneratorCAP : protocols::denovo_design::constraints
• CoordinateConstraintGeneratorCOP : protocols::denovo_design::constraints
• CoordinateConstraintGeneratorOP : protocols::denovo_design::constraints
• CoordinateConstraintStackOP : protocols::protein_interface_design::movers
• Coords : core::chemical::rings
• coords() : protocols::simple_filters
• copy_all_o2prime_torsions() : protocols::stepwise::modeler::rna
• copy_bulge_res_and_sugar_torsion() : protocols::stepwise::modeler::rna::sugar
• COPY_DOF : protocols::stepwise::sampler
• copy_dofs() : core::pose::copydofs
• copy_dofs_match_atom_names() : core::pose::copydofs
• copy_dofs_sort_criterion() : protocols::stepwise::modeler::rna
• copy_helix_bondangles() : protocols::helical_bundle
• copy_helix_bondlengths() : protocols::helical_bundle
• copy_helix_dihedrals() : protocols::helical_bundle
• copy_hotspot_to_pose() : protocols::protein_interface_design::movers
• copy_internal_coords() : protocols::topology_broker
• copy_loop_pose_to_original() : protocols::generalized_kinematic_closure
• copy_over_phosphate_variants() : protocols::stepwise::modeler::rna::phosphate
• copy_pose_crd() : protocols::mpi_refinement
• copy_residue_coordinates_and_rebuild_missing_atoms() : core::conformation
• copy_residues() : protocols::star
• copy_rotamers() : protocols::denovo_design
• copy_side_chains() : protocols::abinitio
• CopyDofMoverCOP : protocols::simple_moves
• CopyDofMoverOP : protocols::simple_moves
• CopyDofsCOP : core::pose::copydofs
• CopyDofsInfoCOP : core::pose::copydofs
• CopyDofsInfoOP : core::pose::copydofs
• CopyDofsOP : core::pose::copydofs
• CopyDofStepWiseSamplerCOP : protocols::stepwise::sampler::copy_dofs
• CopyDofStepWiseSamplerOP : protocols::stepwise::sampler::copy_dofs
• CoreDunbrackFilterCOP : protocols::fldsgn::filters
• CoreDunbrackFilterOP : protocols::fldsgn::filters
• correctly_add_cutpoint_variants() : core::pose , core::pose::rna
• correctly_position_cutpoint_phosphate_torsions() : core::pose::rna
• correctly_position_five_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate
• correctly_position_five_prime_phosphate_SLOW() : protocols::stepwise::modeler::rna::phosphate
• CoulombCOP : core::scoring::etable::coulomb
• CoulombOP : core::scoring::etable::coulomb
• count_AA_w_direction() : protocols::features::strand_assembly
• count_AA_wo_direction() : protocols::features::strand_assembly
• count_atom() : core::scoring::methods
• count_bulges() : protocols::denovo_design
• 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
• count_uniq_char() : protocols::ncbb
• 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
• CoupledMoverCOP : protocols::simple_moves
• CoupledMoverOP : protocols::simple_moves
• covalent_compliance() : protocols::noesy_assign
• CovalentConnectionReplaceInfoCOP : protocols::toolbox::match_enzdes_util
• CovalentConnectionReplaceInfoOP : protocols::toolbox::match_enzdes_util
• CovalentResidueNetworkCOP : protocols::toolbox
• CovalentResidueNetworkOP : protocols::toolbox
• CP_CROSSOVER_3 : core::scoring::etable::count_pair
• CP_CROSSOVER_34 : 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
• CPParameter : core::chemical::rings
• CPResidueConnectionType : core::scoring::etable::count_pair
• Cr : core::chemical::element
• create_acc_orientation_vector() : core::scoring::hbonds
• create_adduct_combinations() : core::chemical
• create_alignment_id_map_legacy() : protocols::stepwise::modeler::align , protocols::stepwise::modeler::rna
• create_alpha_beta_models_table() : protocols::sewing
• create_bond_length() : core::chemical
• 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_entity_resfile_contents() : protocols::pack_daemon
• create_euler_rotation() : protocols::toolbox::rigid_body
• create_ExactSHOEnergy_from_cmdline() : core::scoring::geometric_solvation
• create_extra_output() : protocols::floppy_tail
• create_fragment_set() : protocols::hybridization
• create_fragment_set_no_ssbias() : protocols::hybridization
• create_full_to_input_res_map() : protocols::stepwise::modeler::rna
• create_match_position_modifier() : protocols::match
• create_membrane_docking_foldtree_from_partners() : protocols::membrane
• create_membrane_foldtree_anchor_com() : protocols::membrane
• create_membrane_foldtree_anchor_pose_tmcom() : protocols::membrane
• create_membrane_foldtree_anchor_tmcom() : protocols::membrane
• create_membrane_foldtree_from_anchors() : protocols::membrane
• create_membrane_multi_partner_foldtree_anchor_tmcom() : protocols::membrane
• create_minimization_graph() : core::pack
• create_model_from_pose() : protocols::sewing
• create_oriented_water_rotamer() : core::pack::rotamer_set
• create_packer_graph() : core::pack
• create_pdb_contents_from_sfr() : core::io::pdb
• create_pdb_info_for_single_residue_pose() : core::io::pdb
• create_pdb_line_from_record() : core::io::pdb
• create_record_from_pdb_line() : core::io::pdb
• create_records_from_pdb_file_contents() : core::io::pdb
• create_records_from_pdb_lines() : core::io::pdb
• create_records_from_sfr() : core::io::pdb
• create_remark_headers_from_cstcache() : protocols::enzdes::enzutil
• create_rna_vall_torsions() : protocols::farna
• create_rotamer_descriptor() : core::scoring::hbonds , core::scoring::lkball
• create_rotamer_string() : protocols::stepwise::modeler::rna
• create_sasa_method() : core::scoring::sasa
• create_scmin_minimizer_map() : core::pack
• create_scorefxn() : protocols::stepwise::legacy::modeler::rna
• create_sfr_from_cif_file_op() : core::io::mmcif
• create_sfr_from_pdb_file_contents() : core::io::pdb
• create_sfr_from_pdb_records() : core::io::pdb
• create_shuffle_map_recursive_rms() : core::scoring
• create_specific_membrane_foldtree() : protocols::membrane
• create_standard_o2prime_pack_task() : protocols::stepwise::modeler::rna
• create_strand_list() : protocols::stepwise::modeler::rna
• create_subpose() : core::pose
• create_tag() : protocols::stepwise::modeler::rna
• create_torsion_value_string() : protocols::stepwise::modeler::rna
• create_trie() : core::scoring::trie
• create_working_data() : core::io::pose_from_sfr
• 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
• CRYST1 : core::io::pdb
• CrystalContactsOperationCOP : protocols::toolbox::task_operations
• CrystalContactsOperationOP : protocols::toolbox::task_operations
• crystRMS() : protocols::cryst
• crystRMSfast() : protocols::cryst
• Cs : core::chemical::element
• csa : core::scoring
• csca : core::scoring::rna::chemical_shift
• CSScoreCOP : protocols::frag_picker::scores
• CSScoreOP : protocols::frag_picker::scores
• cst_eq() : core::scoring::constraints
• 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
• CTERM_CONNECT : core::chemical
• ctrl_str_selector() : protocols::environment
• Cu : core::chemical::element
• CubeKey : core::conformation
• CUBIC : protocols::cryst
• 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::init
• CustomScoreSelectorCOP : protocols::frag_picker
• CustomScoreSelectorOP : protocols::frag_picker
• cut_point : protocols::loops
• CutBiasClaimAP : protocols::environment::claims
• CutBiasClaimCAP : protocols::environment::claims
• CutBiasClaimCOP : protocols::environment::claims
• CutBiasClaimerAP : protocols::topology_broker
• CutBiasClaimerCAP : protocols::topology_broker
• CutBiasClaimerCOP : protocols::topology_broker
• CutBiasClaimerOP : protocols::topology_broker
• CutBiasClaimOP : protocols::environment::claims
• CutBiasElements : protocols::environment::claims
• CutChainMoverCOP : protocols::simple_moves
• CutChainMoverOP : protocols::simple_moves
• CutClaimAP : protocols::topology_broker::claims
• CutClaimCAP : protocols::topology_broker::claims
• CutClaimCOP : protocols::topology_broker::claims
• CutClaimOP : protocols::topology_broker::claims
• CutClaims : protocols::topology_broker::claims
• CutElements : protocols::environment::claims
• CUTPOINT_LOWER : core::chemical
• CUTPOINT_OPEN : core::pose::full_model_info
• cutpoint_probabilities() : protocols::medal
• cutpoint_separation() : protocols::antibody
• CUTPOINT_UPPER : core::chemical
• cutpoints_separation() : protocols::antibody
• CycleMoverCOP : protocols::moves
• CycleMoverOP : protocols::moves
• CYCLIC : core::chemical
• CyclicMoverCOP : protocols::moves
• CyclicMoverOP : protocols::moves
• CyclizationMoverCOP : protocols::simple_moves
• CyclizationMoverOP : protocols::simple_moves
• cyclize_pose() : protocols::relax
• CYS_C_ALPHA : core::scoring::disulfides
• CYS_C_BETA : core::scoring::disulfides
• CYS_CEN : core::scoring::disulfides
• CYS_S_GAMMA : core::scoring::disulfides