- c -

• c : core::scoring::fiber_diffraction::FiberDiffraction , core::scoring::fiber_diffraction::FiberDiffractionOptions , core::scoring::saxs::FastSAXSEnergy , protocols::sic_dock::Vec3
• c0 : core::scoring::etable::CubicPolynomial
• C0_ : core::scoring::constraints::BigBinConstraint , core::scoring::etable::coulomb::Coulomb
• c0_ : core::scoring::FACTSRsdTypeInfo
• c1 : core::scoring::etable::CubicPolynomial
• C1_ : core::scoring::constraints::BigBinConstraint , core::scoring::etable::coulomb::Coulomb
• c1_ : core::scoring::FACTSRsdTypeInfo
• c1prime_index_ : core::chemical::rna::RNA_ResidueType
• c2 : core::scoring::etable::CubicPolynomial
• c21 : protocols::normalmode::ContactStruct
• C2_ : core::scoring::etable::coulomb::Coulomb
• c2_ : core::scoring::FACTSRsdTypeInfo
• c2f : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• c2f_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• c2i : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• c2i_ : core::scoring::PoissonBoltzmannPotential
• c2prime_c3prime_bond_length_ : core::scoring::dna::DNATorsionPotential
• c2prime_c3prime_dist_harm_func_ : core::scoring::dna::DNATorsionPotential
• c2prime_c3prime_sd_ : core::scoring::dna::DNATorsionPotential
• c2prime_index_ : core::chemical::rna::RNA_ResidueType
• c3 : core::scoring::etable::CubicPolynomial
• c3_ : core::scoring::FACTSRsdTypeInfo
• c3prime_c2prime_c1prime_angle_harm_func_ : core::scoring::dna::DNATorsionPotential
• c3prime_c2prime_c1prime_bond_angle_ : core::scoring::dna::DNATorsionPotential
• c4prime_c3prime_c2prime_angle_harm_func_ : core::scoring::dna::DNATorsionPotential
• c4prime_c3prime_c2prime_bond_angle_ : core::scoring::dna::DNATorsionPotential
• c4prime_index_ : core::chemical::rna::RNA_ResidueType
• c4prime_o4prime_c1prime_angle_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_angle_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_angle_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_bond_angle_ : core::scoring::rna::RNA_SugarCloseEnergy
• C_ : core::io::CrystInfo , core::scoring::BB_Pos
• c_ : core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::fiber_diffraction::KromerMann
• C_ : core::scoring::func::KarplusFunc , core::scoring::func::PeriodicFunc
• c_ : protocols::cryst::Spacegroup
• C_ : protocols::fldsgn::topology::BB_Pos , protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• c_alpha_centroid_ : protocols::docking::EllipsoidalRandomizationMover
• c_alpha_index_ : core::scoring::disulfides::DisulfideAtomIndices
• c_alpha_non_ellipsoid_centroid_ : protocols::docking::EllipsoidalRandomizationMover
• c_alpha_plane_centroid_ : protocols::docking::EllipsoidalRandomizationMover
• C_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint , protocols::match::upstream::UpstreamResTypeGeometry
• c_axis_ : protocols::docking::EllipsoidalRandomizationMover
• c_beta_index_ : core::scoring::disulfides::DisulfideAtomIndices
• C_bins : core::scoring::dna::DirectReadoutPotential
• c_clusters_ : protocols::pockets::PocketGrid
• c_cyd_seqpos_ : protocols::simple_moves::DisulfideInsertionMover
• C_gbest_ : core::optimization::ParticleSwarmMinimizer
• c_grid_ : protocols::pockets::PocketGrid
• C_index_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• C_inertia_end_ : core::optimization::ParticleSwarmMinimizer
• C_inertia_start_ : core::optimization::ParticleSwarmMinimizer
• C_lbest_ : core::optimization::ParticleSwarmMinimizer
• C_N_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• C_pbest_ : core::optimization::ParticleSwarmMinimizer
• C_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• c_str : protocols::environment::claims::DOFElement
• c_str_ : protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• C_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• c_ter_stem_ : protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• CA : protocols::ub_e2c::ubi_e2c_modeler
• CA1_ : core::scoring::constraints::BigBinConstraint
• CA2_ : core::scoring::constraints::BigBinConstraint
• CA_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CA_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint , protocols::match::upstream::UpstreamResTypeGeometry
• ca_ca_distance_ : protocols::protein_interface_design::movers::LoopFinder
• ca_cb_orients_ : protocols::fldsgn::topology::Sheet
• ca_cprev_n_h_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• ca_cst_ : protocols::seeded_abinitio::CAcstGenerator
• ca_dist_squared_ : protocols::frag_picker::nonlocal::NonlocalFrags
• CA_index_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CA_MASK : core::scoring::electron_density::ElectronDensity
• ca_nnext_c_o_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• CA_only_ : protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::SuperimposeMover
• CA_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• CA_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• cacb_dihedral_tolerance_ : protocols::fldsgn::SheetConstraintGenerator
• cacbcb_angle_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• CaCbCb_angle_scores_ : core::scoring::disulfides::CaCbCb_Angle_Func
• cacbcbca_dihedral_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• CaCbCbCa_dihedral_scores_ : core::scoring::disulfides::CaCbCbCa_Dihedral_Func
• cache_ : core::chemical::ResidueTypeSet , core::fragment::Frame , core::pack::rotamers::SingleResidueRotamerLibraryFactory , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• cache_fragments_ : protocols::forge::components::VarLengthBuild
• cache_limit_ : protocols::canonical_sampling::TrajectoryRecorder , protocols::trajectory::DbTrajectoryWriter
• cache_remarks_ : core::io::silent::SilentStruct
• cache_selection_ : core::select::residue_selector::LayerSelector , core::select::util::SelectResiduesByLayer
• cache_size_ : protocols::features::ReportToDB
• cache_task_ : protocols::protein_interface_design::movers::RandomMutation
• cached_ : protocols::rosetta_scripts::MultiplePoseMover
• cached_aa_ : protocols::denovo_design::connection::BridgeChains
• cached_aa_variants_map_ : core::chemical::ResidueTypeSetCache
• cached_atom_derivs_ : core::scoring::MultipoleElecPotential
• cached_data : protocols::environment::EnvClaimBroker::BrokerResult
• cached_end_ : protocols::denovo_design::connection::BridgeChains
• cached_lookup_result_ : protocols::indexed_structure_store::filters::FragmentLookupFilter
• cached_pose_ : protocols::frag_picker::VallProvider
• cached_pose_by_state_ : core::scoring::methods::PoissonBoltzmannEnergy
• cached_pose_id_ : protocols::frag_picker::VallProvider
• cached_profile_ : protocols::frag_picker::VallProvider
• cached_profile_id_ : protocols::frag_picker::VallProvider
• cached_score_ : protocols::moves::SimulatedTempering
• cached_scores_id_ : protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity
• cached_ss_ : protocols::denovo_design::connection::BridgeChains
• cached_start_ : protocols::denovo_design::connection::BridgeChains
• cached_tries_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• cacher_ : protocols::match::output::MatchCollisionFilter
• calc_ : protocols::filters::CalculatorFilter
• calc_dE_ : protocols::enzdes::RepackWithoutLigandFilter
• calc_freq_temp : core::pack::annealer::SimAnnealerBase
• calc_gdt_ : protocols::comparative_modeling::Align_RmsdEvaluator
• calc_hbond_sasaE_ : protocols::analysis::InterfaceAnalyzerMover
• calc_inter_group_ : protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator
• calc_rms_ : protocols::enzdes::RepackWithoutLigandFilter
• calc_rms_atom_id_map_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• calc_rms_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• calc_rot_freq_ : core::pack::annealer::SimAnnealerBase
• calcenergy : core::scoring::APBSConfig , core::scoring::APBSConfig::I_PARAM
• calcenergy_ : core::scoring::PoissonBoltzmannPotential
• calcforce : core::scoring::APBSConfig::I_PARAM
• calcs_and_calcns_ : protocols::toolbox::task_operations::RestrictByCalculatorsOperation
• calcs_ready_ : protocols::analysis::InterfaceAnalyzerMover
• calculate_silent_Es_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• calculate_suiteness_bonus_ : core::scoring::rna::RNA_SuitePotential
• calculated_ : core::scoring::CenListInfo , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::SigmoidWeightedCenList< T > , protocols::scoring::InterfaceInfo
• calculated_hpatch_deltaE_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculated_surface_deltaE_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• calculator_ : protocols::toolbox::pose_metric_calculators::MetricValueGetter
• calculator_name_ : protocols::multistate_design::MetricCalculatorFitnessFunction , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• calculators_ : core::pose::metrics::CalculatorFactory
• calibration_atom_type_ : protocols::noesy_assign::Resonance
• calibration_constant_ : protocols::noesy_assign::PeakCalibrator
• calibration_constant_highs_ : protocols::noesy_assign::PeakCalibrator
• calibration_constant_lows_ : protocols::noesy_assign::PeakCalibrator
• calibration_convergence_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_cycles_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_eliminate_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_ignore_eliminated_peaks_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_max_noe_dist_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_max_nudging_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_start_nudging_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_stop_nudging_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_target_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_use_median_ : protocols::noesy_assign::PeakAssignmentParameters
• calibrators_ : protocols::noesy_assign::PeakCalibratorMap
• call_order_ : protocols::rosetta_scripts::ParsedProtocol
• Calpha_restraints_ : protocols::ligand_docking::LigandArea
• camelid_ : protocols::antibody::Ab_TemplateInfo , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::Antibody , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::GraftMover
• camelid_constraints_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler
• can_be_deleted_ : protocols::jd2::Job
• candidate_address_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_best_rmsd_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_best_rmsds_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_coords_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_for : protocols::cluster::DataPoint
• candidate_i_ : protocols::frag_picker::nonlocal::NonlocalPair
• candidate_i_rank_ : protocols::frag_picker::nonlocal::NonlocalPair
• candidate_j_ : protocols::frag_picker::nonlocal::NonlocalPair
• candidate_j_rank_ : protocols::frag_picker::nonlocal::NonlocalPair
• candidate_nbr_index_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidates : protocols::cluster::DataPoint
• candidates_sink_ : protocols::frag_picker::FragmentPicker
• candidates_sinks_ : protocols::frag_picker::FragmentPicker
• canonical_ : protocols::farna::libraries::BasePairStepLibrary
• canonical_aas_to_keep_ : core::pack::task::operation::RestrictAbsentCanonicalAASRLT
• canonical_base_pair_step_library_ : protocols::farna::libraries::RNA_LibraryManager
• CAonly_ : protocols::simple_filters::LoopRmsdEvaluator , protocols::simple_filters::SelectRmsdEvaluator
• cap_ends_ : protocols::helical_bundle::BackboneGridSampler
• capping_residues_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• capture_tracer_ : protocols::rpc::JSON_RPC
• carbohydrate_info_ : core::chemical::ResidueType
• carbon_atom : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• carbon_donors_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• carbon_hbond_parameter_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• carbon_hbond_potential_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::ScoringManager
• carbon_types_ : core::scoring::etable::Etable
• careful_base_pair_classifier_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• cart_ : protocols::ncbb::SecStructFinder
• cart_bonded_cutoff_ : protocols::simple_filters::GeometryFilter
• cart_min_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cart_min_graft_ : protocols::antibody::design::AntibodyDesignMover
• cart_resl_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• cart_size_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• cartbonded_ang_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_improper_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_len_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_linear_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_proton_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_tors_ : core::scoring::methods::EnergyMethodOptions
• cartesian_ : core::pack::RTMin , protocols::cryst::SetCrystWeightMover , protocols::relax::RelaxProtocolBase , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::SaneMinMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• cartesian_crossover_ : protocols::simple_moves::CombinePoseMover
• cartesian_minimize_ : protocols::normalmode::NormalModeRelaxMover
• cartesian_minimizer_ : protocols::stepwise::modeler::StepWiseMinimizer
• cartesian_mode_ : protocols::relax::CentroidRelax
• cartfrag_overlap_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol , protocols::seeded_abinitio::SegmentHybridizer
• cartom : protocols::cartesian::MolecularDynamics
• cas_chainA : protocols::simple_filters::SymmetricMotifFilter
• cas_chainB : protocols::simple_filters::SymmetricMotifFilter
• case_lines_ : core::chemical::Metapatch
• cases_ : core::chemical::Metapatch , core::chemical::Patch
• cat_pi_total_ : protocols::toolbox::pose_metric_calculators::CatPiCalculator
• catalytic_atoms_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• catalytic_res_part_of_interface_ : protocols::enzdes::DetectProteinLigandInterface
• catmin_movemap_ : protocols::enzdes::EnzdesFlexBBProtocol
• catmin_mover_ : protocols::enzdes::EnzdesFlexBBProtocol
• catmin_sfxn_ : protocols::enzdes::EnzdesFlexBBProtocol
• catres_only_ : protocols::enzdes::DetectProteinLigandInterface
• catres_packer_weight_ : protocols::enzdes::ProteinLigandInterfaceUpweighter
• CAvar_ : protocols::mpi_refinement::StructAvrgMover
• cavballs : core::scoring::packstat::CavityBallCluster , core::scoring::packstat::SasaResult
• cavity_balls : protocols::vip::VIP_Mover
• cavity_burial_probe_radius_ : protocols::analysis::PackStatMover
• cavity_pose : protocols::vip::VIP_Mover
• CB_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• cb_ : protocols::sic_dock::scores::TrisBpyScore
• cb_angle_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• CB_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint , protocols::match::upstream::UpstreamResTypeGeometry
• CB_b_factor_cutoff_for_electrostatic_interactions_ : protocols::features::strand_assembly::SandwichFeatures
• cb_bias_ : protocols::rigid::RigidBodyMotionMover
• CB_CA_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• cb_dist_cut_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• CB_dist_cutoff_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• cb_distance_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• cb_force_ : protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover
• CB_force_constant_ : core::scoring::constraints::BackboneStubLinearConstraint
• cb_force_constant_ : protocols::protein_interface_design::movers::BestHotspotCstMover
• CB_force_constant_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• CB_index_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CB_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• cbeta12_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cbeta6_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cbeta_den12_ : core::scoring::EnvPairPotential
• cbeta_den6_ : core::scoring::EnvPairPotential
• cbsg_dihedral_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• cbx_ : protocols::frag_picker::VallResidue
• cby_ : protocols::frag_picker::VallResidue
• cbz_ : protocols::frag_picker::VallResidue
• cc_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::sic_dock::scores::TrisBpyScore
• CC_aacen : core::scoring::electron_density::ElectronDensity
• CC_cen : core::scoring::electron_density::ElectronDensity
• cc_func_ : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• ccd_ : protocols::seeded_abinitio::CloseFold
• ccd_close_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• ccd_close_res_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
• ccd_closer_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::screener::ProteinCCD_ClosureScreener
• ccd_cutoff_ : protocols::forge::remodel::RemodelMover::instruction_flags
• ccd_loop_closure_mover_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• ccd_mover_ : protocols::loops::loop_closure::ccd::LoopClosure
• ccd_threshold_ : protocols::antibody::H3PerturbCCD
• ccd_tolerance_ : protocols::farna::movers::RNA_LoopCloser
• ccenter : core::scoring::APBSConfig
• CCs : core::scoring::electron_density::ElectronDensity
• ccw : core::scoring::packstat::Event , core::scoring::packstat::trace
• ccw_angle : core::scoring::packstat::Event
• cd_1b_methods_ : core::scoring::ScoreFunction
• cd_2b_intrares_ : core::scoring::ScoreFunction
• cd_2b_methods_ : core::scoring::ScoreFunction
• cd_2b_pose_ : protocols::match::downstream::ScoringSecMatchRPE
• cd_lr_2b_methods_ : core::scoring::ScoreFunction
• cd_sfxn_ : protocols::simple_moves::GreenPacker
• cdf_ : core::scoring::Ramachandran , protocols::nonlocal::BiasedFragmentMover , protocols::stepwise::sampler::StepWiseSamplerAny
• cdf_by_torsion_bin_ : core::scoring::Ramachandran
• cdr : protocols::antibody::clusters::ClusterData , protocols::antibody::ParatopeMetric< T >
• cdr_ : protocols::antibody::CDRSetOptions , protocols::antibody::clusters::CDRCluster , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions
• cdr_cluster_manager_ : protocols::antibody::AntibodyInfo
• cdr_cluster_set_ : protocols::antibody::AntibodyInfo
• cdr_constraint_ : protocols::antibody::AntibodyModelerProtocol
• cdr_definition : protocols::antibody::AntibodyNumbering
• cdr_definition_ : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• cdr_definition_file_ : protocols::antibody::AntibodyNumberingParser
• cdr_definition_to_enum_ : protocols::antibody::AntibodyEnumManager
• cdr_definition_to_string_ : protocols::antibody::AntibodyEnumManager
• cdr_definition_transform : protocols::antibody::AntibodyNumbering
• cdr_definitions_defined_ : protocols::antibody::AntibodyNumberingParser
• cdr_definitions_defined_using_ : protocols::antibody::AntibodyNumberingParser
• cdr_design_options_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• cdr_dihedral_cst_mover_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignProtocol
• cdr_dock_map_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel
• cdr_graft_design_options_ : protocols::antibody::design::AntibodyDesignMover
• cdr_h3_cut_ : protocols::antibody_legacy::Antibody
• cdr_h3_frags_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• cdr_is_set_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• cdr_landmark_to_enum_ : protocols::antibody::AntibodyEnumManager
• cdr_landmark_to_string_ : protocols::antibody::AntibodyEnumManager
• cdr_loop_ : protocols::antibody::GraftedStemOptimizer
• cdr_loop_end_ : protocols::antibody::CloseOneCDRLoop
• cdr_loop_name_ : protocols::antibody::RefineOneCDRLoop
• cdr_loop_start_ : protocols::antibody::CloseOneCDRLoop
• cdr_name_ : protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop
• cdr_name_to_enum_ : protocols::antibody::AntibodyEnumManager
• cdr_name_to_string_ : protocols::antibody::AntibodyEnumManager
• cdr_numbering : protocols::antibody::AntibodyNumbering
• cdr_options_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• cdr_pdb_numbered_ : protocols::antibody::AntibodyInfo
• cdr_seq_ : protocols::antibody::design::NativeAntibodySeq
• cdr_seq_design_options_ : protocols::antibody::design::AntibodyDesignMover
• cdr_sequence_move_ : protocols::antibody::CDRsMinPackMin
• cdr_set_ : protocols::antibody::design::AntibodyDesignMover
• cdr_set_options_ : protocols::antibody::design::AntibodyDesignMover
• cdr_weight_ : protocols::antibody::design::CDRGraftDesignOptions
• cdrh3_map_ : protocols::antibody::H3RefineCCD
• cdrh_ : protocols::antibody_legacy::Antibody
• cdrl_ : protocols::antibody_legacy::Antibody
• cdrs_ : protocols::antibody::clusters::CDRClusterFeatures , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• cdrs_min_pack_min_ : protocols::antibody::GraftCDRLoopsProtocol
• cdrs_to_apply_ : protocols::antibody::constraints::ParatopeSiteConstraintMover
• cdrs_to_design_ : protocols::antibody::design::AntibodyDesignMover
• cdrs_to_graft_ : protocols::antibody::AntibodyCDRGrafter
• cell_angles : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cell_dimensions : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cell_volume : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cellAngles : core::scoring::electron_density::ElectronDensity
• cellDimensions : core::scoring::electron_density::ElectronDensity
• cen : protocols::kinmatch::KRSQuery , protocols::pockets::SmallMol
• cen1_scorefxn_ : protocols::hybridization::MRMover
• cen2_scorefxn_ : protocols::hybridization::MRMover
• cen_cfg_file_ : core::scoring::saxs::SAXSEnergy
• cen_constraint_ : protocols::ub_e2c::ubi_e2c_modeler
• cen_cst_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::H3PerturbCCD , protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• cen_dist10_pad : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist10_pad_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_hinv : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist10_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_minus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist10_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_plus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist10_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist12_pad : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist12_pad_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_hinv : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist12_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_minus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist12_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_plus : core::scoring::EnvPairPotential
• cen_dist12_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist5_pad : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist5_pad_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_hinv : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist5_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_minus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist5_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_plus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist5_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist6_pad : core::scoring::EnvPairPotential
• cen_dist6_pad_ : core::scoring::membrane::MembraneData
• cen_dist6_pad_hinv : core::scoring::EnvPairPotential
• cen_dist6_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist6_pad_plus : core::scoring::EnvPairPotential
• cen_dist6_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist7_pad : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist7_pad_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_hinv : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist7_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_minus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist7_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_plus : core::scoring::EnvPairPotential , core::scoring::MembranePotential
• cen_dist7_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist_cutoff2 : core::scoring::EnvPairPotential
• cen_dist_cutoff_12_pad : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• cen_distance_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• cen_disulfide_potential_ : core::scoring::ScoringManager
• cen_dst_ : protocols::make_rot_lib::RotData
• cen_hb_potential_ : core::scoring::ScoringManager
• cen_rot_pair_potential_ : core::scoring::ScoringManager
• cen_score_ : protocols::abinitio::IterativeBase
• cen_score_patch_ : protocols::abinitio::IterativeBase
• cen_scorefxn_ : protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover , protocols::relax::CentroidRelax , protocols::seeded_abinitio::CloseFold , protocols::sewing::AssemblyMover
• cen_vdw_ : protocols::ub_e2c::ubi_e2c_modeler
• cend : protocols::simple_moves::LookupResultPlus
• cend_norm : protocols::simple_moves::LookupResultPlus
• Cend_orient_ : protocols::fldsgn::topology::SS_Base
• Cend_pos_ : protocols::fldsgn::topology::SS_Base
• cenfilter_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• cenpack_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cenpack_log_ : core::scoring::EnvPairPotential
• cenrot_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol
• cenrot_libraries_ : core::pack::dunbrack::cenrot::CenrotLibrary
• cenrot_repack_scorefxn_ : protocols::hybridization::CartesianHybridize
• censcale_ : protocols::hybridization::MRMover
• center : core::chemical::rna::GaussianParameter , core::scoring::APBSConfig , core::scoring::packstat::CavityBallCluster , protocols::sparta::RingData
• center_ : core::conformation::UltraLightResidue , core::id::NamedStubID , core::id::StubID , core::scoring::hbonds::HBondEnergy , core::scoring::MembraneEmbed , protocols::docking::membrane::MPDockingMover , protocols::membrane::AddMembraneMover , protocols::membrane::geometry::EmbeddingDef , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembranePositionMover , protocols::qsar::scoring_grid::SingleGrid , protocols::rigid::WholeBodyRotationMover , protocols::viewer::triangle
• center_at_interface_ : protocols::docking::DockingInitialPerturbation
• center_cluster_db_path_ : protocols::antibody::clusters::CDRClusterMatcher
• center_ndx_ : protocols::toolbox::KClusterElement
• center_of_mass_ : core::scoring::rna::RG_Energy_RNA
• center_on_middle_ca_ : protocols::electron_density::DockIntoDensityMover
• center_resnumber_ : protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover
• center_vector_ : protocols::viewer::ConformationViewer
• center_vector_defined_ : protocols::viewer::ConformationViewer
• centers : core::scoring::packstat::PosePackData
• centers_ : core::scoring::packstat::PackingScore , core::scoring::rna::RNA_SuitePotential
• central_atoms_to_score_ : core::scoring::methods::MMBondAngleEnergy , core::scoring::mm::MMBondAngleResidueTypeParamSet
• central_molecule_pdb_ : protocols::simple_moves::PeriodicBoxMover
• central_residue_ : protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• central_residues_ : protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator
• central_resno_ : protocols::simple_moves::PeriodicBoxMover
• centralE : protocols::simple_moves::ThermodynamicData
• centroid_ : core::import_pose::ImportPoseOptions
• centroid_allowed_CSP_fraction_ : protocols::ub_e2c::ubi_e2c_modeler
• centroid_archive_ : protocols::abinitio::IterativeAbrelax
• centroid_bin_max_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_min_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_size_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_CSP_weight_ : protocols::ub_e2c::ubi_e2c_modeler
• centroid_data_ : protocols::make_rot_lib::MakeRotLibOptionsData
• centroid_dG : protocols::analysis::InterfaceData
• centroid_dist_scores_ : core::scoring::disulfides::Cen_Distance_Func
• centroid_input_pose_ : protocols::topology_broker::RigidChunkClaimer
• centroid_loop_mover_str_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_mapping_distance_padding_ : protocols::noesy_assign::PeakAssignmentParameters
• centroid_non_CSP_weight_ : protocols::ub_e2c::ubi_e2c_modeler
• centroid_output_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_relax_ : protocols::surface_docking::SurfaceDockingProtocol
• centroid_score_diff_cut_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_score_ref_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_scorefunction_ : protocols::anchored_design::AnchorMoversData , protocols::floppy_tail::FloppyTailMover , protocols::metal_interface::ZincHeterodimerMover
• centroid_scorefunction_min_ : protocols::anchored_design::AnchorMoversData
• centroid_scorefxn_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_scores_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_screen_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_sfx_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_stage_ : protocols::loop_modeling::LoopModeler
• centroid_vdw_ref_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_weights_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_x : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• centroid_y : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• centroid_z : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• centroids_ : protocols::make_rot_lib::MakeRotLibMover
• centroidscore_filter_ : protocols::protein_interface_design::movers::DockWithHotspotMover
• cenType_ : protocols::simple_moves::StructProfileMover
• cenx_ : protocols::frag_picker::VallResidue
• ceny_ : protocols::frag_picker::VallResidue
• cenz_ : protocols::frag_picker::VallResidue
• cfac : core::scoring::APBSConfig
• cglen : core::scoring::APBSConfig
• cgs_ : protocols::denovo_design::connection::Connection
• ch1_ : protocols::protein_interface_design::movers::LoopFinder
• ch1_begin_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch1_end_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch2_ : protocols::protein_interface_design::movers::LoopFinder
• ch2_begin_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch2_end_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain : core::io::raw_data::DisulfideFile::ResNum , core::scoring::packstat::SimplePDB_Atom , protocols::antibody::design::PDBNumbering , protocols::dna::DnaDesignDef , protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Transform_info
• chain1_ : core::scoring::motif::ResPairMotif , protocols::analysis::InterfaceAnalyzerMover , protocols::denovo_design::connection::BridgeChains , protocols::denovo_design::connection::Connection , protocols::simple_filters::AlaScan
• chain1_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• chain1_letter_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain1_number_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain2_ : core::scoring::motif::ResPairMotif , protocols::analysis::InterfaceAnalyzerMover , protocols::denovo_design::connection::BridgeChains , protocols::denovo_design::connection::Connection , protocols::simple_filters::AlaScan
• chain2_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• chain2_letter_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain2_number_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain_ : core::conformation::Residue , core::fragment::AnnotatedFragData , core::pack::task::operation::ChainIs , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::pose::ResidueIndexDescription , core::scoring::methods::D2H_SA_Energy , protocols::antibody::clusters::CDRCluster , protocols::antibody::PDBLandmark , protocols::features::ResidueGridScoresFeatures , protocols::features::ScreeningFeatures , protocols::frag_picker::frag_movers::FragSetFromH5Mover , protocols::frags::VallData , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::LigandArea , protocols::ligand_docking::MinimizeLigand , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::TetherLigand , protocols::ligand_docking::WriteLigandMolFile , protocols::pmut_scan::MutationData , protocols::pose_length_moves::InsertResMover , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::qsar::qsarMover , protocols::qsar::scoring_grid::GridInitMover , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::SingleGrid , protocols::simple_filters::AngleToVector , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictToTerminiOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• chain_B_resNum_ : protocols::features::strand_assembly::SandwichFragment
• chain_boundaries_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• chain_break_grid_index_screening : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_break_res_ : protocols::topology_broker::AsymFoldandDockClaimer
• chain_break_scorefxn_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• chain_break_screening_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_break_screening_pose_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• chain_closable_geometry_checker_ : protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• chain_closable_geometry_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_closable_geometry_count2 : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_closable_geometry_count3 : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_closable_geometry_screen : protocols::stepwise::modeler::rna::Filterer_Count
• chain_closable_geometry_to_anchor_checker_ : protocols::stepwise::screener::AnchorSugarScreener
• chain_closing_attempts_ : protocols::protein_interface_design::movers::PlaceOnLoop
• chain_closure_checker_ : protocols::stepwise::screener::RNA_ChainClosureScreener
• chain_connections_ : protocols::farna::base_pairs::RNA_BasePairHandler , protocols::farna::movers::RNA_JumpMover , protocols::farna::setup::RNA_DeNovoParameters
• chain_endings_ : core::conformation::Conformation , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• chain_groups_ : protocols::analysis::InterfaceAnalyzerMover
• chain_id : protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Transform_info , protocols::ligand_docking::Translate_info
• chain_id_ : protocols::simple_moves::CutChainMover
• chain_ids_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG , protocols::simple_moves::SwitchChainOrderMover
• chain_ids_to_exclude_ : protocols::ligand_docking::Translate
• chain_letters_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_map : protocols::moves::StructureRestrictor
• chain_name : protocols::antibody::FrameWork
• chain_num_ : protocols::simple_moves::DeleteChainMover , protocols::simple_moves::PSSM2BfactorMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• chain_numbers_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_sequences_ : core::io::StructFileRep
• chain_start_ : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
• chain_strings_ : core::select::residue_selector::ChainSelector
• chain_to_cyclize_ : protocols::simple_moves::CyclizationMover
• chain_to_design_ : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• chainAfterLoop_ : protocols::pose_length_moves::NearNativeLoopCloser
• chainBeforeLoop_ : protocols::pose_length_moves::NearNativeLoopCloser
• chainbreak_max_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• chainbreak_suite_ : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• chainbreak_weight_ : protocols::anchored_design::AnchorMoversData , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• chainbreaks_ : protocols::idealize::IdealizeMover
• chainbreakweights_ : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• chainID : core::io::AtomInformation , core::io::ModifiedResidueInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• chainID1 : core::io::CisPeptideInformation , core::io::LinkInformation , core::io::SSBondInformation
• chainID2 : core::io::CisPeptideInformation , core::io::LinkInformation , core::io::SSBondInformation
• chainID_ : core::io::ResidueInformation
• chainName : protocols::sparta::CORdata
• chains : core::scoring::PQR
• chains_ : core::io::silent::SilentStruct , core::io::StructFileRep , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceScoreCalculator , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops , protocols::simple_moves::DeleteChainsMover
• chains_for_antigen_ : protocols::antibody::AntibodyInfo
• chains_for_cdrs_ : protocols::antibody::AntibodyInfo
• chains_whose_residues_are_separate_chemical_entities_ : core::io::StructFileRepOptions
• chance_of_being_canonical_sw : protocols::features::strand_assembly::SandwichFeatures
• change_chi_without_replacing_residue_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• change_foldtree_ : protocols::protein_interface_design::movers::AddChainBreak
• change_FT_to_flankloop_ : protocols::antibody::H3RefineCCD
• change_FT_to_simpleloop_ : protocols::antibody::H3RefineCCD
• changed_ : core::scoring::FACTSResidueInfo
• changed_residues_ : core::kinematics::ResidueCoordinateChangeList
• changing_baseline_ : protocols::simple_filters::DeltaFilter
• changing_seqpos_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• charge : core::scoring::PQR , protocols::qsar::scoring_grid::ChargeAtom
• charge_ : core::chemical::AddAtom , core::chemical::Atom , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::SetAtomicCharge , core::chemical::SetFormalCharge , core::scoring::elec::ElecAtom
• charge_atom_list_ : protocols::qsar::scoring_grid::ChargeGrid
• charged_ : core::pack::task::operation::ResidueTypeFilter , core::scoring::FACTSRsdTypeInfo
• charged_chains_ : core::scoring::methods::PoissonBoltzmannEnergy
• charged_residues_ : core::scoring::methods::PoissonBoltzmannEnergy
• charged_residues_map_ : core::scoring::methods::PBLifetimeCache
• chbreak_intcpt_ : protocols::abinitio::abscript::AbscriptStageMover
• chbreak_sf_ : protocols::analysis::LoopAnalyzerMover
• chbreak_slope_ : protocols::abinitio::abscript::AbscriptStageMover
• check_abego_ : protocols::denovo_design::connection::Connection
• check_alignment_tolerance_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• check_canonicalness_cutoff_ : protocols::features::strand_assembly::SandwichFeatures
• check_fa_dun_ : protocols::match::upstream::BuildSet
• check_flanking_rms_ : protocols::sewing::LoophashAssemblyMover
• check_frequency_ : protocols::moves::MonteCarlo
• check_if_residues_are_Ctermini_ : core::io::StructFileRepOptions
• check_if_residues_are_Ntermini_ : core::io::StructFileRepOptions
• check_MMT_ : protocols::simple_moves::TorsionDOFMover
• check_N_to_C_direction_by_ : protocols::features::strand_assembly::SandwichFeatures
• check_nucleic_acid_virtual_phosphates_ : core::chemical::ResidueTypeFinder
• check_overlap_ : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• check_pairing_dists_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• check_periodicity_ : protocols::match::downstream::AtomDihedralSecMatchRPE
• check_potential_dsbuilder_incompatibility_ : protocols::match::Matcher
• check_rama_ : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• check_rama_scores_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• check_rmsd_ : protocols::ligand_docking::Transform
• check_ss_ : protocols::simple_moves::ClassicFragmentMover
• check_ss_lengths_ : protocols::frags::TorsionFragmentMover
• check_tolerance_ : protocols::farna::movers::RNA_LoopCloser
• checkpoint_ : protocols::abinitio::MembraneAbinitio , protocols::forge::remodel::RemodelMover::instruction_flags
• checkpoint_count_ : protocols::boinc::Boinc , protocols::canonical_sampling::MetropolisHastingsMover
• checkpoint_filename_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• checkpoint_gz_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• checkpoint_gzip_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• checkpoint_ids_ : protocols::abinitio::MembraneAbinitio , protocols::canonical_sampling::MetropolisHastingsMover , protocols::checkpoint::CheckPointer
• checkpoint_interval_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• checkpoint_job_identifier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• checkpoint_prefix_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• checkpoint_rename_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• checkpoint_write_interval_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• checkpointer_ : protocols::abinitio::abscript::AbscriptMover::StageTracker
• checkpointfile_ : protocols::frag_picker::nonlocal::NonlocalFrags
• checkpointing_file_ : protocols::simple_filters::ReportFilter
• checkpoints_ : protocols::abinitio::FragmentSampler , protocols::abinitio::Protocol , protocols::loophash::Mover_LoopHashRefine , protocols::loops::loop_mover::LoopMover , protocols::relax::ClassicRelax , protocols::relax::FastRelax
• checkpoints_map_ : protocols::frag_picker::nonlocal::NonlocalFrags
• chem_shift_scorefxn_ : protocols::farna::RNA_FragmentMonteCarlo
• CHEMICAL : core::kinematics::Edge
• chemical_name_ : core::chemical::Element
• chemical_symbol_ : core::chemical::Element
• chemshift_column_ : protocols::abinitio::IterativeBase
• chemshift_overlap_ : protocols::noesy_assign::PeakAssignment
• chemshift_overlap_weight_ : protocols::noesy_assign::PeakAssignmentParameters
• chgm : core::scoring::APBSConfig::I_PARAM
• chi : core::pack::dunbrack::ChiSet
• chi1_ : core::scoring::motif::ResPairMotif
• chi2 : core::scoring::saxs::FastSAXSEnergy
• chi2_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::motif::ResPairMotif
• CHI2_ANGLES : protocols::sparta::Sparta::SpartaLib
• chi2max_ : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• chi2min_ : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• chi_ : core::conformation::Residue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::RotamerExplosion , core::scoring::motif::Xfres , protocols::dna::DNABase , protocols::dna::DnaInterfaceMinMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::optimize_weights::PNatRotOptERotamerData , protocols::simple_moves::MinimalRotamer , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes
• chi_2_proton_chi_ : core::chemical::ResidueType
• chi_angles_ : protocols::sewing::SewResidue
• chi_atoms_ : core::chemical::ResidueType
• chi_atoms_indices_ : core::chemical::ResidueType
• chi_chain1_ : protocols::seeded_abinitio::SeedSetupMover
• chi_chain2_ : protocols::seeded_abinitio::SeedSetupMover
• chi_clones_ : core::conformation::symmetry::SymmetryInfo
• chi_dev_ : protocols::comparative_modeling::Align_RotamerEvaluator
• chi_diff_threshold_ : protocols::dna::PDBOutput
• CHI_energy_function_ : core::scoring::ScoringManager
• chi_follows_ : core::conformation::symmetry::SymmetryInfo
• chi_mean_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_min_ : protocols::enzdes::EnzdesBaseProtocol
• chi_no_ : core::chemical::ClearChiRotamers
• chi_north_potential_guanosine_ : core::scoring::rna::RNA_TorsionPotential
• chi_north_potential_others_ : core::scoring::rna::RNA_TorsionPotential
• chi_number_pseudoalpha_ : core::chemical::rna::RNA_ResidueType
• chi_number_pseudobeta_ : core::chemical::rna::RNA_ResidueType
• chi_number_pseudoepsilon_ : core::chemical::rna::RNA_ResidueType
• chi_number_pseudogamma_ : core::chemical::rna::RNA_ResidueType
• chi_number_pseudozeta_ : core::chemical::rna::RNA_ResidueType
• chi_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• chi_potential_syn_guanosine_bonus_ : core::scoring::rna::RNA_TorsionPotential
• chi_purine_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_purine_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_pyrimidine_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_pyrimidine_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_ranges_ : protocols::make_rot_lib::MakeRotLibOptionsData
• chi_rmsd_ : core::scoring::motif::MotifHit
• chi_rotamer_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• chi_rotamers_ : core::chemical::ResidueType
• chi_sample_level_ : core::pack::task::EX
• chi_samplers_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• chi_samples_ : protocols::match::upstream::FullChiSampleSet
• chi_sd_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_south_potential_guanosine_ : core::scoring::rna::RNA_TorsionPotential
• chi_south_potential_others_ : core::scoring::rna::RNA_TorsionPotential
• chi_start_for_active_residue_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• chi_torsions_ : core::io::silent::RNA_SilentStruct
• chi_xx_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xy_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xz_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_yy_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_yz_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chibin_combo_indexer_ : protocols::match::output::SameChiBinComboGrouper
• chidev_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• chidevpen_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• child_mover_ : protocols::ligand_docking::UnconstrainedTorsionsMover
• children : core::kinematics::Node
• children_ : protocols::loop_modeling::LoopMover
• chimean_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• chimera_ : protocols::sewing::SewSegment
• chino_ : core::chemical::AddChi , core::chemical::AddChiRotamer , core::chemical::AddProtonChi , core::chemical::RedefineChi
• chinum_ : protocols::simple_moves::sidechain_moves::SetChiMover
• chiral_seq_pos_ : protocols::simple_moves::chiral::ChiralMover
• chirality_ : protocols::simple_moves::chiral::ChiralMover
• chirality_sign_ : core::scoring::MultipoleParameter
• chisd_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• chitip_atoms_ : protocols::match::upstream::UpstreamResTypeGeometry
• choices_ : protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• choose_best_solution_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• choose_least_perturb_solution_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• choose_random_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• choose_random_solution_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• chunk_ : protocols::frag_picker::FragmentCandidate
• chunk_atoms_xyz_ : protocols::frag_picker::scores::AtomBasedConstraintsScore
• chunk_ca_distances_ : protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::PCS_FragDistance
• chunk_coordinates_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• chunk_coverage_ : protocols::farna::libraries::RNA_ChunkLibrary , protocols::farna::RNA_FragmentMonteCarlo
• chunk_gunn_data_ : protocols::frag_picker::scores::GunnCostScore
• chunk_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• chunk_key_ : protocols::frag_picker::VallChunk
• chunk_pdb_files_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• chunk_phi_ : protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell
• chunk_psi_ : protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell
• chunk_sets_ : protocols::farna::libraries::RNA_ChunkLibrary
• chunk_silent_files_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• chunks_ : protocols::frag_picker::FragmentPicker , protocols::frag_picker::VallProvider , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::nonlocal::SingleFragmentMover , protocols::rigid::RigidBodyMotionMover
• Ci_ : core::scoring::FACTSResidueInfo
• ci_1b_methods_ : core::scoring::ScoreFunction
• ci_2b_intrares_ : core::scoring::ScoreFunction
• ci_2b_methods_ : core::scoring::ScoreFunction
• ci_lr_2b_methods_ : core::scoring::ScoreFunction
• ci_rpes_ : protocols::simple_moves::GreenPacker
• ci_sfxn_ : protocols::simple_moves::GreenPacker
• ciBR_only_ : core::pack::annealer::FASTERAnnealer , protocols::pack_daemon::FASTER_IG_Repacker
• cif_files_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• circle : core::scoring::packstat::Event , core::scoring::packstat::trace
• circles_ : core::scoring::packstat::LeeRichards , core::scoring::packstat::Slice
• cis_chi4_mean_ : core::scoring::methods::ProClosureEnergy
• cis_chi4_sd_ : core::scoring::methods::ProClosureEnergy
• cis_omega_ : core::sequence::ABEGO , protocols::idealize::IdealizeMover
• CIS_OMG_LOWER_RANGE : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• CIS_OMG_UPPER_RANGE : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• cis_packed_rotno_2_sorted_rotno_ : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• cis_rotamers_ : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• cis_trans_conf : protocols::antibody::clusters::ClusterData
• cis_trans_match_ : protocols::antibody::clusters::CDRCluster
• CIS_UPPER_TRANS_LOWER_SPLIT : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• cispep_map_ : core::io::StructFileRep
• claim_backbone_ : protocols::environment::claims::TorsionClaim
• claim_list_ : protocols::environment::ScriptCM
• claim_right_ : protocols::topology_broker::FragmentClaimer
• claim_sidechain_ : protocols::environment::claims::TorsionClaim
• claim_source_ : protocols::environment::claims::EnvClaim , protocols::topology_broker::claims::DofClaim
• claimer_ : protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::topology_broker::RigidBodyRandomTMHMover
• claimers_ : protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimerFactory
• claims_ : protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::RigidChunkCM , protocols::environment::EnvClaimBroker
• clash : protocols::kinmatch::KRSQuery
• clash_check_ : core::scoring::motif::ResPairMotifQuery , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::TryRotamers
• clash_count : protocols::sewing::HashResult
• clash_dis : protocols::sic_dock::CBScoreVisitor
• clash_dis_ : protocols::sic_dock::CBScore
• clash_dis_sq : protocols::sic_dock::CorrectionVisitor
• clash_dist_ : protocols::matdes::ClashCheckFilter
• clash_dist_cutoff_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• clash_residues_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• clash_score : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• clash_score_cutoff_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• clash_scorefxn_ : protocols::sewing::RepeatAssemblyMover
• clash_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• clash_threshold_ : protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• clash_wt_ : protocols::simple_filters::SymmetricMotifFilter
• classification_ : core::io::HeaderInformation
• classifier : core::pose::rna::RNA_SuiteInfo
• ClassType : protocols::sparta::GDB
• CLD : protocols::sic_dock::SICFast
• CLD2 : protocols::sic_dock::SICFast
• clear_all_residues_ : protocols::flxbb::FlxbbDesign
• clear_bprots_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• clear_seeds_ : protocols::seeded_abinitio::CAcstGenerator
• client_ : protocols::environment::ScriptCM
• cliques_ : protocols::features::clique_saver
• close_ : protocols::dna::DnaNeighbor
• close_chain_ : protocols::stepwise::screener::PartitionContactScreener
• close_chbrk_ : protocols::abinitio::ClassicAbinitio
• close_loops_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::movers::RNA_Minimizer , protocols::farna::options::RNA_FragmentMonteCarloOptions
• close_loops_after_each_move_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• close_loops_in_last_round_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• close_threshold_ : protocols::dna::DnaInterfaceFinder , protocols::dna::RestrictDesignToProteinDNAInterface
• closed_loop_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• closer_ft : protocols::environment::EnvClaimBroker::BrokerResult
• closest_rsd_ : protocols::membrane::AddMPLigandMover
• closest_state_on_alt_bb_ : protocols::flexpack::interaction_graph::FlexbbNode
• closure_fragments_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• closure_frame_ : protocols::loops::loop_closure::ccd::LoopClosure
• closure_protocol_ : protocols::abinitio::KinematicAbinitio
• cluster : protocols::antibody::CDRDBPose , protocols::antibody::CDRDBSequence , protocols::antibody::clusters::ClusterData
• cluster_ : core::scoring::packstat::CavityBall , protocols::antibody::clusters::CDRCluster , protocols::forge::remodel::RemodelAccumulator
• cluster_base_ : protocols::cluster::AssignToClustersMover
• cluster_based_CDRDBPose_indexes_ : protocols::antibody::design::AntibodyDesignMover
• cluster_by_all_atom_ : protocols::cluster::GatherPosesMover
• cluster_by_all_atom_rmsd_ : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cluster_by_protein_backbone_ : protocols::cluster::GatherPosesMover
• cluster_center_ : protocols::cluster::Cluster
• cluster_centers_neighbor_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• cluster_data_ : protocols::antibody::clusters::CDRClusterMatcher
• cluster_data_cutoff_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• cluster_manager_ : protocols::antibody::CDRSetOptionsParser
• cluster_matcher_ : protocols::antibody::clusters::CDRClusterSet
• cluster_min_volume : core::scoring::packstat::SasaOptions
• cluster_num_ : protocols::make_rot_lib::RotData
• cluster_oversample_ : protocols::electron_density::DockIntoDensityMover
• cluster_radius : protocols::toolbox::ClusterOptions
• cluster_radius_ : protocols::cluster::ClusterBase , protocols::electron_density::DockIntoDensityMover , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::toolbox::ClusterPhilStyle
• cluster_rmsd_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::options::StepWiseBasicOptions
• cluster_rmsds_to_try_with_auto_tune_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• cluster_size_ : protocols::stepwise::modeler::align::StepWiseClusterer
• cluster_switch_ : protocols::forge::remodel::RemodelAccumulator
• clusterer_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• clusterlist : protocols::cluster::ClusterBase
• clusterlist_ : protocols::toolbox::ClusterBase
• clusters_ : protocols::antibody::clusters::BasicCDRClusterSet , protocols::antibody::clusters::CDRClusterSet , protocols::pockets::CClusterSet , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• cmd_ : core::io::external::PsiPredInterface , protocols::denovo_design::filters::SSPredictionFilter , protocols::simple_filters::HolesFilter
• cmd_line_csts_ : protocols::comparative_modeling::LoopRelaxMover
• cmd_line_operation_ : protocols::antibody::design::GeneralAntibodyModeler
• coarse_angle_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• coarse_centering_mode : core::scoring::APBSConfig::I_PARAM
• coarse_rna_ : protocols::farna::libraries::RNA_ChunkLibrary
• coarse_rna_name_to_num_ : protocols::coarse_rna::CoarseRNA_Fragments
• coarse_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• code_to_root_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• coef1_ : protocols::branch_angle::BranchAngleOptimizer
• coef2_ : protocols::branch_angle::BranchAngleOptimizer
• coef_ : protocols::forge::constraints::NtoCConstraintGenerator
• COEF_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• coef_map1_ : protocols::branch_angle::BranchAngleOptimizer
• coef_map2_ : protocols::branch_angle::BranchAngleOptimizer
• coeff_grad_x : core::scoring::electron_density::ElectronDensity
• coeff_grad_y : core::scoring::electron_density::ElectronDensity
• coeff_grad_z : core::scoring::electron_density::ElectronDensity
• coeffs_ : protocols::sasa_scores::Poly
• coeffs_density_ : core::scoring::electron_density::ElectronDensity
• col2islabel_ : protocols::noesy_assign::PeakFileFormat
• col2proton_ : protocols::noesy_assign::PeakFileFormat
• col_name_ : protocols::simple_filters::JScoreEvaluator
• collector_ : protocols::frag_picker::quota::QuotaSelector
• collision_check_id_2_restype_id_ : protocols::toolbox::match_enzdes_util::LigandConformer
• colonyE_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• color_ : protocols::qsar::RenderGridsToKinemage
• color_data_ : protocols::qsar::RenderGridsToKinemage
• Color_mode : protocols::viewer::GraphicsState
• color_mode_ : protocols::qsar::RenderGridsToKinemage
• color_name : protocols::qsar::ColorGradient
• color_value : protocols::qsar::ColorGradient
• coloumb_ : protocols::ligand_docking::rdf::RDFElecFunction
• column_labels_ : protocols::noesy_assign::PeakFileFormat
• column_names_ : protocols::contact_map::ContactMap , protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• column_width_ : protocols::rotamer_recovery::RRReporterHuman
• com : core::scoring::methods::RG_MinData
• COM : protocols::toolbox::DecoySetEvaluation
• com_ : protocols::features::helixAssembly::HelicalFragment
• CoM_ : protocols::pockets::FingerprintBase
• com_jump_name_ : protocols::environment::CoMTrackerCM
• com_name_ : protocols::environment::CoMTrackerCM
• COM_target_ : protocols::constraints_additional::COMCoordinateConstraint
• com_vector_criterion_ : protocols::match::NumNeighborsMPM
• comatms : core::scoring::elec::ElecGroup
• combine_exclude_res_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• combine_helical_silent_file_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• combine_history_ : protocols::simple_moves::CombinePoseMover
• combine_long_loop_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• combine_ratio_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• combine_resis_ : protocols::enzdes::PoseFoundResiduesCombination
• combine_score : protocols::stepwise::modeler::rna::Combine_Tags_Info
• combined_filters_ : protocols::matdes::MatDesGreedyOptMutationMover
• COMM_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• comm_size_ : protocols::canonical_sampling::AsyncMPITemperingBase
• command : protocols::relax::RelaxScriptCommand
• command_ : protocols::rpc::JSON_RPC , protocols::simple_filters::ExternalEvaluator
• commands_ : core::pack::task::ResfileContents
• comment : core::io::ModifiedResidueInformation
• comment_exists_ : protocols::simple_filters::PoseComment
• comment_lines_ : core::io::silent::SilentFileData
• comment_name_ : protocols::simple_filters::PoseComment
• comment_value_ : protocols::simple_filters::PoseComment
• comments_ : core::io::rna::RDAT , core::sequence::SequenceAlignment
• COMMIT_LIMIT_BETWEEN_UPDATES : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• COMMON_DENOMINATOR : core::scoring::ResidualDipolarCoupling
• communicator_handle_ : protocols::jd2::MPIMultiCommJobDistributor
• comp : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• comp1_ids_ : protocols::denovo_design::connection::Connection
• comp2_ids_ : protocols::denovo_design::connection::Connection
• comp_constraint_aas_ : protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential
• compact_residue_schema_ : protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures
• comparator_ : protocols::frag_picker::BestTotalScoreSelector , protocols::frag_picker::CustomScoreSelector
• compare_all_to_ground_state_ : protocols::multistate_design::PartitionAggregateFunction< T >
• compare_energy_to_ground_state_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• compare_to_ref_ : protocols::matdes::SymUnsatHbondFilter
• comparer_ : protocols::features::RotamerRecoveryFeatures , protocols::rotamer_recovery::RotamerRecovery
• comparer_name_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• comparer_params_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• comparer_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• complete_moving_atom_id_map_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• completed_ : protocols::jd2::Job , protocols::jd3::LarvalJob
• completed_first_round1_hit_building_ : protocols::match::downstream::ClassicMatchAlgorithm
• complex_total_energy : protocols::analysis::InterfaceData
• complexed_energy : protocols::analysis::PerResidueInterfaceData
• complexed_interface_score : protocols::analysis::InterfaceData
• complexed_SASA : protocols::analysis::InterfaceData
• complexed_sasa : protocols::analysis::PerResidueInterfaceData
• component_bounds_ : core::conformation::symmetry::SymmetryInfo
• component_id_ : protocols::frag_picker::CompareScoreComponent
• component_membership_ : core::pack::interaction_graph::InteractionGraphBase
• component_weights_ : protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEMultifunc
• components_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo , protocols::frag_picker::CompareByScoreCombination , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• CompositeSegmentMoveSet_ : protocols::rbsegment_relax::RBSegmentRelax
• compound_factory_ : protocols::toolbox::task_operations::StoreCompoundTaskMover
• compound_filters_ : protocols::matdes::MatDesGreedyOptMutationMover
• compound_in_progress_ : core::io::HeaderInformation
• compound_statement_ : protocols::filters::CompoundFilter
• compound_task_ : protocols::toolbox::task_operations::StoreCompoundTaskMover
• compounds_ : core::io::HeaderInformation
• compprob_ : core::scoring::packstat::PackingScore
• compute_entropy_reduction_ : protocols::simple_filters::RotamerBoltzmannWeight
• compute_grid_scores_ : protocols::ligand_docking::InterfaceScoreCalculator
• compute_interface_delta_hbond_unsat_ : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_energy_ : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_sc_ : protocols::analysis::InterfaceAnalyzerMover
• compute_max_ : protocols::simple_filters::RotamerBoltzmannWeight
• compute_mg_sol_for_hydrogens_ : core::scoring::magnesium::MgEnergy
• compute_packstat_ : protocols::analysis::InterfaceAnalyzerMover , protocols::features::InterfaceFeatures
• compute_rmsd_ : protocols::comparative_modeling::LoopRelaxMover
• compute_separated_sasa_ : protocols::analysis::InterfaceAnalyzerMover
• computed_ : core::scoring::DenseEnergyContainer , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::OneToAllEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedEnergyContainer
• concave : core::scoring::sc::_RESULTS
• condist_ : protocols::fldsgn::NcontactsCalculator
• condition_ : protocols::protein_interface_design::movers::LoopOver
• cone_angle_cos_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• conf_ : core::environment::DofPassport , core::pose::PDBInfo , protocols::viewer::ConformationViewer
• conf_event_link_ : protocols::boinc::BoincCurrentPoseObserver
• conf_num_ : protocols::docking::DockingEnsemble
• conf_size_ : protocols::docking::DockingEnsemble
• confidence_ : core::fragment::SecondaryStructure , protocols::filters::StochasticFilter
• config : core::scoring::APBSWrapper
• config_file_ : protocols::topology_broker::TemplateFragmentClaimer
• config_filename_ : core::scoring::PoissonBoltzmannPotential
• conformation : core::conformation::signals::ConnectionEvent , core::conformation::signals::GeneralEvent
• conformation_ : core::pose::Pose , core::scoring::func::ConformationXYZ , protocols::environment::DofUnlock
• conformation_event_link_ : protocols::moves::PyMolObserver
• conformation_obs_hub_ : core::pose::Pose
• conformation_pt_ : core::scoring::constraints::ConstraintSet
• conformation_size : core::conformation::signals::LengthEvent
• conformations_for_flexible_segments_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• conformer_found_ : protocols::carbohydrates::LinkageConformerMover
• conformer_group_for_conformer_ : protocols::match::downstream::LigandConformerBuilder
• conformer_group_indices_ : protocols::match::downstream::LigandConformerBuilder
• conformer_sets_ : core::chemical::ResidueType
• Conformers : protocols::sparta::PDB
• conformers_ : core::chemical::rings::RingConformerManager
• conjug_ : core::chemical::Bond
• conjugated_ : core::chemical::gasteiger::GasteigerAtomTypeData
• conn_id_ : core::chemical::ResConnID
• connect_atom_ : core::chemical::AddConnect
• connect_from_ : protocols::protein_interface_design::movers::SetAtomTree
• connect_info_cutoff_ : core::io::StructFileRepOptions
• connect_map_ : core::conformation::Residue
• connect_to_ : protocols::protein_interface_design::movers::SetAtomTree
• connected_by_twobonds_ : core::scoring::methods::GoapRsdType
• connected_indices : core::io::AtomInformation
• connected_resonance_ids_ : protocols::noesy_assign::Resonance
• connected_resonance_ptrs_ : protocols::noesy_assign::Resonance
• connecting_bond_dist_ : protocols::denovo_design::connection::Connection
• connection_atom_sets_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_distance_ : core::scoring::etable::etrie::CountPairData_1_1
• connection_distances_ : core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3
• connection_event_link_ : protocols::viewer::ConformationViewer
• connection_gaps_ : core::scoring::etable::etrie::TrieCountPairGeneric
• connection_id_ : protocols::ligand_docking::AddHydrogen
• connection_index_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_obs_hub_ : core::conformation::Conformation
• connection_theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_use_theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connections_to_residues_ : core::conformation::Residue
• cons_design_data_source_ : protocols::antibody::task_operations::AddCDRProfilesOperation
• cons_task_ : protocols::antibody::task_operations::AddCDRProfilesOperation
• conservation_ : core::pose::datacache::PositionConservedResiduesStore
• conservation_cutoff_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• conservation_cutoff_aligned_segments_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• conservation_cutoff_protein_interface_design_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• conserve_foldtree_ : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• conserved_mutations_ : protocols::toolbox::task_operations::ConservativeDesignOperation
• conserved_pos_taskop_ : protocols::simple_filters::ConservedPosMutationFilter
• consider_already_bonded_ : protocols::cyclic_peptide::TryDisulfPermutations
• consider_topN_frags_ : protocols::simple_moves::StructProfileMover
• considered_energy_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• considered_node_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• considered_state_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• consolidate_matches_ : protocols::match::MatcherTask
• const_data_cache_ : protocols::jd3::InnerLarvalJob
• CONST_SCORE : protocols::frag_picker::scores::ConstScore
• constant_cache_ : core::pose::Pose
• constrain_ : protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover
• constrain_bb_angle_ : protocols::fldsgn::SheetConstraintGenerator
• constrain_bb_cacb_dihedral_ : protocols::fldsgn::SheetConstraintGenerator
• constrain_bb_dihedral_ : protocols::fldsgn::SheetConstraintGenerator
• constrain_ca_ca_dist_ : protocols::fldsgn::SheetConstraintGenerator
• constrain_coords_ : protocols::relax::RelaxProtocolBase
• constrain_cter_ : protocols::antibody::AntibodyModelerProtocol
• constrain_relax_segments_ : protocols::relax::RelaxProtocolBase
• constrain_relax_to_native_coords_ : protocols::relax::RelaxProtocolBase
• constrain_relax_to_start_coords_ : protocols::relax::RelaxProtocolBase
• constrain_vlvh_qq_ : protocols::antibody::AntibodyModelerProtocol
• constrainable_atoms_ : protocols::frag_picker::scores::AtomBasedConstraintsScore
• constrained_lig_atoms_ : protocols::enzdes::EnzdesConstraintReporter
• constrained_nonligand_atoms_ : protocols::enzdes::EnzdesConstraintReporter
• constraint_ : protocols::aa_composition::AddCompositionConstraintMover
• constraint_cutoff_ : protocols::docking::DockingLowResFilter
• constraint_definition : protocols::forge::remodel::LineObject
• constraint_file_ : protocols::fldsgn::BluePrintBDR
• constraint_func_ : protocols::forge::constraints::InverseRotamersRCG
• constraint_ref_pose_ : protocols::topology_broker::ConstraintClaimer
• constraint_reporter_ : protocols::enzdes::PredesignPerturbMover
• constraint_set_ : core::pose::Pose , core::scoring::constraints::CstEnergyContainer , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_FragmentMonteCarlo
• constraint_set_high_res_ : protocols::simple_moves::ConstraintSetMover
• constraint_set_low_res_ : protocols::simple_moves::ConstraintSetMover
• constraint_threshold_ : protocols::abinitio::FoldConstraints
• constraint_weight_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::simple_moves::DisulfideInsertionMover
• constraint_weights_ : protocols::enzdes::EnzdesBaseProtocol
• constraints_ : core::scoring::constraints::Constraints , core::scoring::constraints::CstMinimizationData , protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::ShowViolation , protocols::constraints_additional::ConstraintEvaluator , protocols::hotspot_hashing::HotspotStubSet , protocols::ligand_docking::LigandDockMain , protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• constraints_combine_ratio_ : protocols::constraints_additional::ConstraintEvaluator
• constraints_from_link_records_ : core::io::StructFileRepOptions
• constraints_NtoC_ : protocols::fldsgn::BluePrintBDR , protocols::flxbb::FlxbbDesign
• constraints_only_ : protocols::idealize::IdealizeMover
• constraints_ready_ : core::scoring::dna::DNATorsionEnergy
• constraints_sheet_ : protocols::fldsgn::BluePrintBDR , protocols::flxbb::FlxbbDesign
• contact_ : protocols::dna::DnaNeighbor
• contact_buried_problematic_res_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• contact_dis : protocols::sic_dock::CBScoreVisitor
• contact_dis_ : protocols::sic_dock::CBScore
• contact_dist2_ : protocols::fldsgn::filters::InterlockingAromaFilter
• contact_dist_ : protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::ExtractSubposeMover , protocols::matdes::InterfacePackingFilter
• contact_dist_cutoff_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• contact_list_ : protocols::scoring::Interface
• contact_threshold_ : protocols::dna::DnaInterfaceFinder , protocols::dna::RestrictDesignToProteinDNAInterface
• contact_types_ : protocols::frag_picker::FragmentPicker
• contacts : protocols::sic_dock::CorrectionVisitor
• contacts_ : protocols::contact_map::ContactMap , protocols::frag_picker::nonlocal::NonlocalPair
• contacts_between_ssElement_threshold_ : protocols::simple_filters::SSElementMotifContactFilter
• contacts_dist_cutoff_squared_ : protocols::frag_picker::FragmentPicker
• contacts_dist_cutoffs_squared_ : protocols::frag_picker::FragmentPicker
• contacts_min_seq_sep_ : protocols::frag_picker::FragmentPicker
• contains_carbohydrate_residues_ : core::conformation::Conformation
• contents_ : protocols::checkpoint::FileBuffer
• context_dependent_ : core::scoring::elec::FA_GrpElecEnergy
• context_derivative_empty_ : core::scoring::FACTSPoseInfo
• context_graphs_ : core::scoring::Energies
• context_graphs_required_ : core::scoring::ScoreFunctionInfo
• context_minstrength_ : core::scoring::elec::FA_GrpElecEnergy
• context_pdbname_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• context_pose_ : protocols::flexpack::OtherContextScoreFunction
• context_poses_ : protocols::optimize_weights::IterativeOptEDriver
• context_update_step_ : protocols::md::MDBase
• contiguous_monomers_ : core::conformation::symmetry::SymmetryInfo
• continuous_ : core::scoring::methods::GoapEnergy
• controlling_chi_for_atom_ : protocols::match::upstream::UpstreamResTypeGeometry
• conventional_chains_ : core::pose::full_model_info::FullModelParameters
• conventional_numbering_ : core::pose::full_model_info::FullModelParameters
• convergence_checks_ : protocols::moves::MonteCarlo
• convert_scores_to_probabilities_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• convex : core::scoring::sc::_RESULTS
• coor : core::scoring::sc::_DOT
• coor_constraint_stack_ : protocols::protein_interface_design::movers::PlaceStubMover
• coor_cst_cutoff_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• Coord : protocols::sparta::CORdata
• coord_constrain_sidechains_ : protocols::relax::RelaxProtocolBase
• coord_cst_std_ : protocols::protein_interface_design::movers::PlaceStubMover
• coord_cst_weight_ : protocols::farna::movers::RNA_Minimizer
• coord_csts_ : protocols::protein_interface_design::movers::CoordinateConstraintStack
• coord_dev_ : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• coord_frame_ref_ : core::scoring::MultipoleElecResidueInfo
• coord_sdev_ : protocols::farna::movers::RNA_Minimizer , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• coord_type_ : core::scoring::MultipoleParameter
• coordA : protocols::sparta::RingData
• coordinate_cacher_ : protocols::match::output::PDBWriter , protocols::match::output::WriteKinemageOutputter
• coordinate_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• coordinate_constraint_weight_ : protocols::abinitio::LoopJumpFoldCst , protocols::idealize::IdealizeMover
• coordinate_constraint_weights_ : protocols::abinitio::LoopJumpFoldCst
• coordinate_constraints_during_minimize_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• coordinates : protocols::pockets::SmallMol
• coordinates_ : core::chemical::rotamers::StoredRotamerLibrarySpecification
• coordinates_assigned_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• coords_ : core::conformation::UltraLightResidue , core::fragment::BBTorsionSRFD , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::scmin::ResidueAtomTreeCollectionMomento , core::pose::MiniPose , core::pose::UnrecognizedAtomRecord , core::sequence::Cell , protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , protocols::match::downstream::TargetRotamerCoords , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::sewing::SewAtom , protocols::toolbox::DecoySetEvaluation
• coords_for_clash_checking_ : protocols::match::downstream::TargetRotamerCoords
• coords_receiving_buffer_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• coords_transfer_buffer_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• copy_all_chi_ : protocols::simple_moves::ReturnSidechainMover
• copy_begin : protocols::forge::remodel::RemodelWorkingSet
• copy_comments_ : protocols::simple_filters::RelativePoseFilter
• copy_DOF_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• copy_dof_movers_ : protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler
• copy_dofs_ : protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler
• copy_dofs_info_ : core::pose::copydofs::CopyDofs , protocols::simple_moves::CopyDofMover
• copy_dofs_rotamer_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• copy_end : protocols::forge::remodel::RemodelWorkingSet
• copy_o2prime_hydrogens_ : protocols::stepwise::modeler::packer::SideChainCopier
• copy_pdbinfo_ : protocols::grafting::GraftMoverBase , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::ReplaceRegionMover
• copy_res_ : protocols::stepwise::modeler::packer::SideChainCopier
• copy_sidechains_ : protocols::comparative_modeling::LoopRelaxMover , protocols::seeded_abinitio::SwapSegment
• copy_ss_torsion_only_ : protocols::hybridization::InsertChunkMover
• copy_stretch_ : protocols::simple_filters::RelativePoseFilter
• COradius2_ : core::scoring::FACTSRsdTypeInfo
• core15_ : protocols::abinitio::IterativeBase
• core2_ : protocols::abinitio::IterativeBase
• core3_ : protocols::abinitio::IterativeBase
• core4_ : protocols::abinitio::IterativeBase
• core_ : protocols::simple_filters::LoopRmsdEvaluator , protocols::toolbox::task_operations::SelectBySASAOperation
• core_asa_ : protocols::toolbox::task_operations::SelectBySASAOperation
• core_chunks_ : protocols::hybridization::HybridizeFoldtreeDynamic
• core_cutoff_ : protocols::toolbox::pose_metric_calculators::SequenceComparison
• correct_LJtruncation_ : protocols::simple_moves::PeriodicBoxMover
• correction : protocols::sic_dock::CorrectionVisitor
• correspondence_ : protocols::pack_daemon::PackDaemon
• correspondence_file_name_ : protocols::pack_daemon::StructureFileNames
• corresponding_atom_id_map_ : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• corresponding_res_block_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• corresponding_res_num_in_block_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• cos_flipped_ANGLE_CUTOFF_HIGH : core::scoring::methods::LK_SigmoidalFunc
• cos_flipped_ANGLE_CUTOFF_LOW : core::scoring::methods::LK_SigmoidalFunc
• cos_r_cell_angles : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cosAHD_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• cosAHD_long_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosAHD_short_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosBAH_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• cosBAH_long_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosBAH_short_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosRcellAngles : core::scoring::electron_density::ElectronDensity
• cost_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::simple_moves::SmoothFragmentMover
• coulomb_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::GroupElec , core::scoring::rna::StackElecEnergy
• count : protocols::make_rot_lib::running_average_pair
• count_ : core::scoring::motif::ResPairMotif , protocols::contact_map::Contact , protocols::features::TopCountOfAllInputs , protocols::features::TopCountOfEachInput , protocols::noesy_assign::FragsToAtomDist::DistanceRecord , protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• count_AA_with_direction_ : protocols::features::strand_assembly::SandwichFeatures
• count_as_percentage_ : protocols::simple_filters::ResidueCountFilter
• count_checkpoint_recoveries_ : protocols::checkpoint::CheckPointer
• count_data_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::BaseCentroidScreener
• count_decoys_ : protocols::noesy_assign::DistanceScoreMover
• count_eps_ : protocols::simple_filters::NMerSVMEnergyFilter
• count_grid_ : protocols::canonical_sampling::BiasEnergy
• count_per_rotamer_combo_ : protocols::match::output::LimitHitsPerRotamerFilter
• count_recovered_ : protocols::optimize_weights::IterativeOptEDriver
• count_rotamer_for_lastseen_restype_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• count_rotamers_per_target_restype_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• count_rotamers_recovered_ : protocols::optimize_weights::IterativeOptEDriver
• count_sc_hbonds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• count_viols_ : core::scoring::func::CountViolFunc , core::scoring::func::SkipViolFunc
• count_water_ : core::select::residue_selector::NumNeighborsSelector
• counter_ : protocols::kinematic_closure::pivot_pickers::StandardPivots , protocols::moves::MonteCarlo
• counters_ : protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::canonical_sampling::TrialCounterObserver
• counts_ : protocols::canonical_sampling::SimulatedTempering , protocols::frag_picker::ContactCounts
• couplings_ : core::pack::rotamer_set::RotamerCouplings
• cov_bond_only_flag_ : protocols::ub_e2c::ubi_e2c_modeler
• covalent_bonds_ : protocols::denovo_design::components::StructureData
• covalent_compliance_ : protocols::noesy_assign::PeakAssignment
• covalent_compliance_weight_ : protocols::noesy_assign::PeakAssignmentParameters
• covalent_connections_ : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• covalent_distances_ : protocols::noesy_assign::CovalentCompliance
• coverage_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• covered_by_chunk_ : protocols::farna::libraries::RNA_ChunkLibrary
• cp_data_ : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA >
• cp_half : core::scoring::etable::count_pair::CountPairFunction
• CP_parameters : core::chemical::rings::RingConformer
• cp_rep_map_ : core::scoring::elec::FA_ElecEnergy
• cp_rep_map_byname_ : core::scoring::elec::FA_ElecEnergy
• cpfxn_weight_ : core::scoring::elec::GroupElec
• cprev_n_bond_length_params_ : core::scoring::methods::ResidueCartBondedParameters
• cpu_time : protocols::boinc::BoincSharedMemory
• cpu_time_ : protocols::boinc::Boinc
• cRad : protocols::pockets::PocketExemplarMultifunc
• create_db_ : protocols::loophash::LoopHashLibrary
• create_reference_data_ : protocols::simple_moves::GreenPacker
• create_vrt_p1_ : protocols::environment::claims::JumpClaim
• create_vrt_p2_ : protocols::environment::claims::JumpClaim
• creator_map_ : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::pack::rotamers::SingleResidueRotamerLibraryFactory , core::select::residue_selector::ResidueSelectorFactory
• cross_angle_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::topology::HelixPairing
• cross_over_ : protocols::fldsgn::topology::BetaAlphaBetaMotif
• cross_peaks_ : protocols::noesy_assign::DistanceScoreMover
• cross_val_ : core::scoring::ProQPotential
• crossing_angle : protocols::features::helixAssembly::FragmentPair
• crossover_ : core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::etrie::TrieCountPairGeneric
• crosspeak_ : protocols::noesy_assign::PeakAssignment
• crosspeaks_ : protocols::noesy_assign::NoesyModule
• crossterm_interface_energy : protocols::analysis::InterfaceData
• crossterm_interface_energy_dSASA_ratio : protocols::analysis::InterfaceData
• cryst1_ : protocols::simple_moves::symmetry::SetupForSymmetryMover
• crystinfo_ : core::io::StructFileRep , core::pose::PDBInfo
• CS_RAD_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• CS_RCY_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• CS_RGU_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• CS_URA_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• cs_verbose_mode_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• csa_bank_size_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• csa_rmsd_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• csa_score_ : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• CSAerr_ : core::scoring::CSA
• CSAval_ : core::scoring::CSA
• CSAval_computed_ : core::scoring::CSA
• csequence_ : protocols::seeded_abinitio::GrowPeptides
• csf_cbang1_ : core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::CBSG_Dihedral_Func
• csf_cbang1a_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang1b_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang2_ : core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::CBSG_Dihedral_Func
• csf_cbang2a_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang2b_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang3_ : core::scoring::disulfides::CBSG_Dihedral_Func
• CSP_ : protocols::ub_e2c::ubi_e2c_modeler
• CSP_swap_trim_ : protocols::ub_e2c::ubi_e2c_modeler
• CSP_trim_ : protocols::ub_e2c::ubi_e2c_modeler
• cst_ : core::scoring::constraints::Obsolet_NamedAtomPairConstraint , protocols::md::Rattle
• cst_action_ : protocols::enzdes::AddOrRemoveMatchCsts
• cst_block_ : protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• cst_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• cst_conformers_ : protocols::jumping::ResiduePairJump
• cst_cutoff_ : protocols::simple_filters::GeometryFilter
• cst_data_ : protocols::abinitio::IterativeBase
• cst_fa_data_ : protocols::abinitio::IterativeBase
• cst_fa_file_ : protocols::simple_moves::ConstraintSetMover
• cst_fa_weight_ : protocols::docking::DockingProtocol
• cst_file_ : protocols::hybridization::FoldTreeHybridize , protocols::membrane::MPQuickRelaxMover , protocols::relax::RangeRelaxMover , protocols::simple_moves::ConstraintSetMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• cst_file_name_ : protocols::simple_moves::SequenceProfileMover
• cst_filename_ : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• cst_files_ : protocols::relax::RelaxProtocolBase
• cst_func_ : protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::topology_broker::CoordConstraintClaimer
• cst_graph_ : core::scoring::constraints::CstEnergyContainer
• cst_io_ : protocols::match::output::OutputWriter
• cst_jumps_ : protocols::jumping::ResiduePairJump
• cst_lib_ : protocols::constraints_additional::CombinedConstraintEvaluator
• cst_map_ : protocols::moves::ConstraintGenerator
• cst_max_seq_sep_ : core::scoring::methods::EnergyMethodOptions
• cst_opt_ : protocols::enzdes::EnzRepackMinimize
• cst_pairs_ : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• cst_params : protocols::relax::CentroidRelax::parameters
• cst_pose_ : protocols::topology_broker::CoordConstraintClaimer
• cst_score_types_ : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::KofNConstraint
• cst_sd_ : protocols::relax::AtomCoordinateCstMover
• cst_sdev_ : protocols::md::MDBase , protocols::normalmode::NormalModeRelaxMover
• cst_seqwidth_ : protocols::rbsegment_relax::RBSegmentRelax
• cst_set_ : core::pose::full_model_info::FullModelParameters , protocols::ddg::ddGMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::StepWiseModeler
• cst_set_revision_id_ : core::scoring::constraints::CstEnergyContainer
• cst_sfx_ : protocols::forge::remodel::RemodelLigandHandler
• cst_sidechain_ : protocols::relax::AtomCoordinateCstMover
• cst_source_ : protocols::constraints_additional::ConstraintEvaluator
• cst_stdev_ : protocols::rbsegment_relax::RBSegmentRelax
• cst_strength_ : protocols::noesy_assign::PeakAssignmentParameters
• cst_string_ : core::pose::full_model_info::FullModelParameters
• cst_to_native_ : protocols::relax::RangeRelaxMover
• cst_to_start_ : protocols::relax::RangeRelaxMover
• cst_type_ : protocols::protein_interface_design::movers::TaskAwareCsts
• cst_types_ : core::scoring::constraints::ConstraintFactory
• cst_weight : protocols::simple_moves::ShakeStructureMover
• cst_weight_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::docking::DockingProtocol , protocols::membrane::MPQuickRelaxMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::RangeRelaxMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover
• cst_width_ : protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::AtomCoordinateCstMover
• cstAtoms_ : protocols::jumping::ResiduePairJumpSingle
• cstblocksize_ : protocols::forge::remodel::RemodelEnzdesCstModule
• cstfile_ : protocols::abinitio::Template , protocols::enzdes::AddOrRemoveMatchCsts , protocols::forge::remodel::RemodelMover::instruction_flags
• cstfile_map_ : protocols::enzdes::AddOrRemoveMatchCsts
• cstfile_name_ : protocols::match::MatcherTask , protocols::match::output::PDBWriter
• cstid_ : protocols::enzdes::EnzScoreFilter
• cstid_list_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::RepackWithoutLigandFilter
• cstInfoMap_ : protocols::jumping::ResiduePairJump
• cstres_interactions_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• csts_ : protocols::moves::ConstraintGenerator , protocols::sic_dock::ConstraintSetScore
• csts_from_frags_ : protocols::hybridization::HybridizeProtocol
• cstset_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::Template
• cstw : protocols::mpi_refinement::MethodParams
• cstyle_A_ : protocols::scoring::methods::pcs2::PcsDataLanthanide
• cstyle_b_ : protocols::scoring::methods::pcs2::PcsDataLanthanide
• cstyle_b_individual_scale_ : protocols::scoring::methods::pcs2::PcsDataLanthanide
• ct_ : protocols::abinitio::hConvergenceCheck , protocols::hybridization::hConvergenceCheck
• ctab_mode_ : core::chemical::sdf::MolWriter
• cter_insert_ : protocols::antibody::AntibodyModelerProtocol
• Cter_insert_flexibility_ : protocols::grafting::AnchoredGraftMover
• Cter_loop_end_ : protocols::grafting::AnchoredGraftMover
• Cter_loop_start_ : protocols::grafting::AnchoredGraftMover
• cter_overhang_ : protocols::antibody::AntibodyCDRGrafter , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::KeepRegionMover
• Cter_overhang_length_ : protocols::grafting::GraftMoverBase
• Cter_scaffold_flexibility_ : protocols::grafting::AnchoredGraftMover
• cTerm_cap_size_ : protocols::simple_moves::RepeatPropagationMover
• cterm_included_ : protocols::denovo_design::components::Segment
• cterm_length_ : protocols::match::RemoveNorCTermMPM
• cterm_rsd_num_ : protocols::simple_moves::CyclizationMover
• cube_dim_ : protocols::scoring::ImplicitFastClashCheck
• cube_dim_ca_ : protocols::scoring::ImplicitFastClashCheck
• cubes : core::scoring::packstat::Octree2D
• cubes_ : protocols::scoring::ImplicitFastClashCheck
• cubes_ca_ : protocols::scoring::ImplicitFastClashCheck
• cull_list_ : protocols::abinitio::Templates
• cum_dist6_ : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• cum_dist_ : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• cummulative_time_ : protocols::md::MDBase
• cumulate_jobs_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulate_prob_ : protocols::hybridization::CartesianSampler
• cumulate_replicas_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulated_jobs_ : protocols::jd2::MPIFileBufJobDistributor
• cumulated_runtime_ : protocols::jd2::MPIFileBufJobDistributor
• cumulative_ : protocols::hybridization::FragmentBiasAssigner
• cumulative_peak_volume_ : protocols::noesy_assign::CrossPeak
• cumulative_sums_ : protocols::frag_picker::scores::AdaptiveScoreHistogram
• cur_energy_ : protocols::flexpack::interaction_graph::FlexbbEdge
• cur_indices_ : protocols::helical_bundle::BackboneGridSamplerHelper , protocols::helical_bundle::BundleGridSamplerHelper
• cur_ncluster_ : protocols::toolbox::KMedoid
• curr_ : core::chemical::AutomorphismIterator
• curr_bg_bg_exhpobeolap_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• curr_bin_ : protocols::match::VoxelSetIterator
• curr_coordinate_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover
• curr_dots_cache_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• curr_exemplar : protocols::cluster::DataPoint
• curr_gen_entities_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• curr_idx_ : core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator
• curr_in_recent_history_ : core::pack::annealer::FASTERAnnealer
• curr_jobid_ : protocols::jobdist::BaseJobDistributor
• curr_loop_end_ : protocols::protein_interface_design::movers::PlaceOnLoop
• curr_memory_for_rpes_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• curr_min_bb_ : protocols::simple_moves::DesignRepackMover
• curr_min_rb_ : protocols::simple_moves::DesignRepackMover
• curr_min_sc_ : protocols::simple_moves::DesignRepackMover
• curr_mut_filename : protocols::ddG::ddGData
• curr_mut_read : protocols::ddG::ddGData
• curr_pos_ : protocols::match::VoxelSetIterator
• curr_pose_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::GrowPeptides
• curr_rot_2_orig_rot_ : protocols::simple_moves::GreenPacker
• curr_rotamer_ : protocols::stepwise::sampler::StepWiseSamplerAny
• curr_rotamers_with_correspondence_ : protocols::simple_moves::GreenPacker
• curr_rotamers_without_correspondence_ : protocols::simple_moves::GreenPacker
• curr_sc_centroid_ : core::pack::interaction_graph::SimpleNode
• curr_sc_radius_ : core::pack::interaction_graph::SimpleNode
• curr_score_log : protocols::relax::SRelaxPose
• curr_state_ : protocols::stepwise::sampler::StepWiseSamplerSizedAny
• curr_state_energy_ : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• curr_state_exolap_hphobes_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G >
• curr_state_exp_hphobes_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_inv_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_one_body_energy_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_sparse_mat_info_ : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• curr_state_total_energy_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_total_hASA_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• curr_state_two_body_energies_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• curr_wt_filename : protocols::ddG::ddGData
• curr_wt_read : protocols::ddG::ddGData
• current_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• current_address_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• current_address_str_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• current_angles_ : protocols::matdes::SymDofMoverSampler
• current_batch_ : protocols::jd2::BatchJobInputter
• current_batch_id_ : protocols::jd2::JobDistributor
• current_best_rmsds_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• current_chain_pair_pose_ : protocols::analysis::PeptideDeriverPoseOutputter
• current_claims_ : protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• current_cycle_ : protocols::features::TrajectoryMapFeatures
• current_cycle_number_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• current_distance_ : core::scoring::loop_graph::LoopScoreInfo
• current_embedding_ : protocols::membrane::TransformIntoMembraneMover
• current_end : protocols::antibody_legacy::Antibody
• current_energy_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SimpleEdge , protocols::simple_moves::sidechain_moves::SidechainMCMover
• current_exchange_schedule_ : protocols::canonical_sampling::HamiltonianExchange
• current_filename_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream
• current_func_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• current_generation_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_gs_ : protocols::viewer::ConformationViewer
• current_ig_ : protocols::simple_moves::GreenPacker
• current_index_ : core::import_pose::pose_stream::MetaPoseInputStream
• current_input_stream_ : core::import_pose::pose_stream::MetaPoseInputStream
• current_inter_group_packer_neighbor_graph_ : protocols::simple_moves::GreenPacker
• current_intra_group_packer_neighbor_graph_ : protocols::simple_moves::GreenPacker
• current_job_ : protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor , protocols::moves::Mover
• current_job_id_ : protocols::jd2::JobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• current_jump_ : protocols::simple_moves::symmetry::SymmetrySlider
• current_jump_calculator_ : protocols::topology_broker::RigidChunkClaimer
• current_jumps_ : protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::RigidChunkClaimer
• current_kinematics_ : protocols::abinitio::KinematicTaskControl
• current_loop_is_H3_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• current_maximum_id_ : core::environment::EnvCore
• current_mode_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• current_n_ : core::import_pose::pose_stream::ExtendedPoseInputStream
• current_noesy_sampling_file_ : protocols::abinitio::IterativeBase
• current_nstruct_ : protocols::jd2::MSDJobDistributor , protocols::jobdist::BaseJobDistributor
• current_ntrial_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• current_one_body_energy_ : core::pack::interaction_graph::SimpleNode
• current_packer_neighbor_graph_ : protocols::simple_moves::GreenPacker
• current_partner_chain_letter_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverPoseOutputter
• current_pep_length_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• current_pep_length_cyclic_peptide_encountered_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• current_peptide_length_ : protocols::analysis::PeptideDeriverPoseOutputter
• current_pose_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::jd2::MSDJobDistributor , protocols::simple_moves::MSDMover , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyBroker
• current_pose_buf : protocols::boinc::BoincSharedMemory
• current_pose_energy_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• current_pose_exists : protocols::boinc::BoincSharedMemory
• current_pose_ghost_buf : protocols::boinc::BoincSharedMemory
• current_pose_ghost_exists : protocols::boinc::BoincSharedMemory
• current_pose_loop_score_info_ : core::scoring::loop_graph::LoopGraph
• current_position_ : core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• current_radial_disps_ : protocols::matdes::SymDofMoverSampler
• current_receptor_chain_letter_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverPoseOutputter
• current_residue_ : core::pack::interaction_graph::SimpleNode
• current_residues_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• current_rigid_core_ : protocols::topology_broker::RigidChunkClaimer
• current_rot_index_ : core::pack::annealer::SimAnnealerBase
• current_rotamer_copy_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• current_rotamer_sets_ : protocols::simple_moves::GreenPacker
• current_rotamers_ : protocols::simple_moves::GreenPacker
• current_score : protocols::relax::SRelaxPose , protocols::stepwise::modeler::rna::output_data_struct
• current_score_ : protocols::simple_moves::GenericMonteCarloMover
• current_score_cutoff_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• current_sequence_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• current_start : protocols::antibody_legacy::Antibody
• current_state_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• current_state_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchEdge< V, E, G >
• current_state_info_ : protocols::flexpack::interaction_graph::FlexbbNode
• current_state_rotamer_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• current_struct : protocols::relax::SRelaxPose
• current_struct_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream
• current_tag_ : protocols::moves::Mover
• current_tags_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• current_task_ : protocols::simple_moves::GreenPacker
• current_temp_ : protocols::canonical_sampling::TemperingBase
• current_to_pick_ : core::pack::annealer::RotamerAssigningAnnealer
• current_total_isc_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• current_trajectory_state_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• current_transform_ : protocols::antibody::AntibodyInfo
• current_trial_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::flxbb::FilterStructs
• custom_angle_ : protocols::backrub::BackrubMover
• custom_rama_map_ : protocols::simple_moves::SetTorsion
• custom_rama_table_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• custom_residue_types_ : core::chemical::ResidueTypeSet
• custom_structure_input_tag_ : protocols::features::ReportToDB
• custom_structure_tag_ : protocols::features::ReportToDB
• custom_variant_types_ : core::chemical::ResidueProperties
• custom_variants_ : core::chemical::ResidueTypeFinder
• cut : protocols::loops::SerializedLoop
• cut1_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::SecondaryMatchProtocol
• cut2_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::SecondaryMatchProtocol
• cut3_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::SecondaryMatchProtocol
• cut4_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::SecondaryMatchProtocol
• cut_ : protocols::environment::claims::JumpClaim , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::loops::Loop , protocols::rbsegment_relax::CCDMoveWrapper
• cut_bias_ : protocols::topology_broker::CutBiasClaimer
• cut_bond_ : core::chemical::Bond
• cut_bond_neighbor_ : core::chemical::ResidueType
• cut_bond_neighbor_indices_ : core::chemical::ResidueType
• cut_off_born_radius_ : core::scoring::FACTSPotential
• cut_point : protocols::stepwise::modeler::rna::Jump_point
• cut_points_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::SeedFoldTree
• cut_prob_ : protocols::jumping::JumpsFromAllPairings
• cut_reg_ : protocols::jumping::JumpSetup::JumpDef , protocols::jumping::ResiduePairJumpSetup::JumpDef
• cut_resis_ : protocols::denovo_design::connection::Connection
• cutoff_ : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::enzdes::ValueEvaluator , protocols::frag_picker::DiversifyCrmsdSelector , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::SidechainContactDistCutoff , protocols::ligand_docking::LigandArea , protocols::qsar::qsarOptFunc , protocols::qsar::scoring_grid::VdwGrid , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_moves::FragmentCost , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• cutoff_3_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• cutoff_9_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• cutoff_cst_score_ : core::scoring::constraints::KofNConstraint
• cutoff_distance_ : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• cutoff_flag_ : protocols::match::downstream::ScoringSecMatchRPE
• cutoff_lower_ : core::scoring::func::FadeFunc
• cutoff_lr_ : core::scoring::CenHBPotential
• cutoff_scoreType_flag_ : protocols::match::downstream::ScoringSecMatchRPE
• cutoff_squared_ : protocols::frag_picker::SidechainContactDistCutoff
• cutoff_sr_ : core::scoring::CenHBPotential
• cutoff_upper_ : core::scoring::func::FadeFunc
• cutoffE_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• cutpoint : protocols::denovo_design::CutAndJump
• cutpoint_ : core::kinematics::FoldTree , protocols::antibody::H3RefineCCD , protocols::denovo_design::components::Segment , protocols::simple_moves::ChainSplitMover
• cutpoint_closed_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• cutpoint_closed_list_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• cutpoint_map_ : core::kinematics::FoldTree
• cutpoint_open_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• cutpoint_open_list_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• cutpoint_res_ : protocols::loops::LoopFromFileData
• cutpoint_suite_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• cutpoints_ : protocols::star::Extender
• cutpoints_closed_ : protocols::farna::setup::RNA_DeNovoParameters
• cutpoints_open_ : protocols::farna::base_pairs::RNA_BasePairHandler , protocols::farna::setup::RNA_DeNovoParameters
• cutpos_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• cutpos_list_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• cuts_ : protocols::jumping::JumpSample , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::topology_broker::TMHTopologySamplerClaimer
• cw_angle : core::scoring::packstat::Event
• cycle_counts_ : protocols::features::TrajectoryReportToDB
• cycle_selector_ : protocols::noesy_assign::PeakAssignmentParameters
• cycles : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Transform_info , protocols::ligand_docking::Translate_info
• cycles_ : core::scoring::loop_graph::cycle_printer , protocols::abinitio::abscript::AbscriptStageMover , protocols::farna::FARNA_Optimizer , protocols::grafting::AnchoredGraftMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::magnesium::MgMonteCarlo , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::movers::LoopRemodel , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::RangeRelaxMover , protocols::sewing::GreedyAssemblyMover , protocols::sewing::MonteCarloAssemblyMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• cycles_adjust_ : protocols::abinitio::abscript::AbscriptStageMover
• cycles_inner_ : protocols::dna::DesignProteinBackboneAroundDNA
• cycles_outer_ : protocols::dna::DesignProteinBackboneAroundDNA
• cyclic_oxygen_ : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_index_ : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_name_ : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_peptides_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• cyclic_permutations_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication