- c -

• c : protocols::sic_dock::Vec3
• c21 : protocols::normalmode::ContactStruct
• C_ : protocols::fldsgn::topology::BB_Pos , protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• c_alpha_centroid_ : protocols::docking::EllipsoidalRandomizationMover
• c_alpha_non_ellipsoid_centroid_ : protocols::docking::EllipsoidalRandomizationMover
• c_alpha_plane_centroid_ : protocols::docking::EllipsoidalRandomizationMover
• C_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• c_axis_ : protocols::docking::EllipsoidalRandomizationMover
• c_clusters_ : protocols::pockets::PocketGrid
• c_grid_ : protocols::pockets::PocketGrid
• C_index_ : protocols::fldsgn::topology::BB_Pos
• 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_ter_stem_ : protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• CA : protocols::ub_e2c::ubi_e2c_modeler
• CA_ : protocols::fldsgn::topology::BB_Pos
• CA_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• ca_ca_distance_ : protocols::protein_interface_design::movers::LoopFinder
• ca_cb_orients_ : protocols::fldsgn::topology::Sheet
• ca_cst_ : protocols::seeded_abinitio::CAcstGenerator
• ca_dist_squared_ : protocols::frag_picker::nonlocal::NonlocalFrags
• CA_index_ : protocols::fldsgn::topology::BB_Pos
• CA_only_ : protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::SuperimposeMover
• CA_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• cacb_dihedral_tolerance_ : protocols::fldsgn::SheetConstraintsRCG
• cache_ : protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity , protocols::wum2::WorkUnit
• cache_fragments_ : protocols::forge::components::VarLengthBuild
• cache_limit_ : protocols::canonical_sampling::TrajectoryRecorder , protocols::trajectory::DbTrajectoryWriter
• cache_size_ : protocols::features::ReportToDB
• cache_task_ : protocols::protein_interface_design::movers::RandomMutation
• cached_ : protocols::rosetta_scripts::MultiplePoseMover
• cached_data : protocols::environment::EnvClaimBroker::BrokerResult
• cached_lookup_result_ : protocols::indexed_structure_store::filters::FragmentLookupFilter
• cached_pose_ : protocols::frag_picker::VallProvider
• 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
• cacher_ : protocols::match::output::MatchCollisionFilter
• calc_ : protocols::filters::CalculatorFilter
• calc_dE_ : protocols::enzdes::RepackWithoutLigandFilter
• calc_gdt_ : protocols::comparative_modeling::Align_RmsdEvaluator
• calc_hbond_sasaE_ : protocols::analysis::InterfaceAnalyzerMover
• 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
• calcs_and_calcns_ : protocols::toolbox::task_operations::RestrictByCalculatorsOperation
• calcs_ready_ : protocols::analysis::InterfaceAnalyzerMover
• calculate_silent_Es_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• calculated_ : protocols::scoring::InterfaceInfo
• calculated_atom_id_domain_map_ : protocols::toolbox::AllowInsert
• calculator_ : protocols::toolbox::pose_metric_calculators::MetricValueGetter
• calculator_name_ : protocols::multistate_design::MetricCalculatorFitnessFunction , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• 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
• 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
• CAonly_ : protocols::simple_filters::LoopRmsdEvaluator , protocols::simple_filters::SelectRmsdEvaluator
• capping_residues_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• capture_tracer_ : protocols::rpc::JSON_RPC
• cart_bonded_cutoff_ : protocols::simple_filters::GeometryFilter
• cart_min_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cartesian_ : 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::hybridization::HybridizeSetup , protocols::seeded_abinitio::SegmentHybridizer
• cartmin_ : protocols::antibody::design::AntibodyDesignMoverGenerator
• cartom : protocols::cartesian::MolecularDynamics
• cas_chainA : protocols::simple_filters::SymmetricMotifFilter
• cas_chainB : protocols::simple_filters::SymmetricMotifFilter
• 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
• cavity_balls : protocols::vip::VIP_Mover
• cavity_burial_probe_radius_ : protocols::analysis::PackStatMover
• cavity_pose : protocols::vip::VIP_Mover
• CB_ : protocols::fldsgn::topology::BB_Pos
• cb_ : protocols::sic_dock::scores::TrisBpyScore
• CB_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• CB_b_factor_cutoff_for_electrostatic_interactions_ : protocols::features::strand_assembly::SandwichFeatures
• cb_bias_ : protocols::rigid::RigidBodyMotionMover
• cb_dist_cut_ : protocols::simple_filters::DomainInterfaceFilter
• CB_dist_cutoff_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• 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_ : protocols::protein_interface_design::movers::BestHotspotCstMover
• CB_force_constant_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• CB_index_ : protocols::fldsgn::topology::BB_Pos
• cbx_ : protocols::frag_picker::VallResidue
• cby_ : protocols::frag_picker::VallResidue
• cbz_ : protocols::frag_picker::VallResidue
• cc_ : protocols::sic_dock::scores::TrisBpyScore
• 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::RNA_LoopCloser
• cd_2b_pose_ : protocols::match::downstream::ScoringSecMatchRPE
• cd_sfxn_ : protocols::simple_moves::GreenPacker
• cdf_ : protocols::nonlocal::BiasedFragmentMover , protocols::stepwise::sampler::StepWiseSamplerAny
• cdr : protocols::antibody::clusters::ClusterData , protocols::antibody::ParatopeMetric< T >
• cdr_ : protocols::antibody::CDRSetOptions , protocols::antibody::clusters::CDRCluster , 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_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_dock_map_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel
• cdr_graft_design_options_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyGraftDesignMover
• cdr_h3_cut_ : protocols::antibody_legacy::Antibody
• cdr_h3_frags_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• 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_design_options_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• cdr_sequence_move_ : protocols::antibody::CDRsMinPackMin
• cdr_set_ : protocols::antibody::design::AntibodyGraftDesignMover
• cdr_set_options_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyGraftDesignMover
• 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
• cdrs_min_pack_min_ : protocols::antibody::GraftCDRLoopsProtocol
• cdrs_to_apply_ : protocols::antibody::constraints::ParatopeSiteConstraintMover
• cen : protocols::kinmatch::KRSQuery , protocols::pockets::SmallMol
• cen1_scorefxn_ : protocols::hybridization::MRMover
• cen2_scorefxn_ : protocols::hybridization::MRMover
• cen_constraint_ : protocols::ub_e2c::ubi_e2c_modeler
• cen_cst_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::H3PerturbCCD , protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• cen_dst_ : protocols::make_rot_lib::RotData
• 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
• cen_vdw_ : protocols::ub_e2c::ubi_e2c_modeler
• Cend_orient_ : protocols::fldsgn::topology::SS_Base
• Cend_pos_ : protocols::fldsgn::topology::SS_Base
• cenfilter_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• censcale_ : protocols::hybridization::MRMover
• center : protocols::sparta::RingData
• center_ : 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_vector_ : protocols::viewer::ConformationViewer
• center_vector_defined_ : protocols::viewer::ConformationViewer
• central_residue_ : protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• central_residues_ : protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator
• 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_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
• cenx_ : protocols::frag_picker::VallResidue
• ceny_ : protocols::frag_picker::VallResidue
• cenz_ : protocols::frag_picker::VallResidue
• ch1_ : protocols::protein_interface_design::movers::LoopFinder
• ch2_ : protocols::protein_interface_design::movers::LoopFinder
• chain : protocols::antibody::design::PDBNumbering , protocols::dna::DnaDesignDef , protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Transform_info
• chain1_ : protocols::analysis::InterfaceAnalyzerMover , protocols::simple_filters::AlaScan
• chain2_ : protocols::analysis::InterfaceAnalyzerMover , protocols::simple_filters::AlaScan
• chain_ : protocols::antibody::clusters::CDRCluster , protocols::antibody::PDBLandmark , protocols::features::ResidueGridScoresFeatures , protocols::features::ScreeningFeatures , 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::loops::ResidueIndexDescription , protocols::pmut_scan::MutationData , 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::RNA_StructureParameters
• 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
• 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::PSSM2BfactorMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• chain_numbers_ : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_order_ : protocols::simple_moves::SwitchChainOrderMover
• chain_start_ : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
• 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
• 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::RNA_DeNovoProtocol , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• chainbreaks_ : protocols::idealize::IdealizeMover
• chainbreakweights_ : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• chainName : protocols::sparta::CORdata
• chains_ : protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceScoreCalculator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• chains_for_antigen_ : protocols::antibody::AntibodyInfo
• chains_for_cdrs_ : protocols::antibody::AntibodyInfo
• 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
• changing_baseline_ : protocols::simple_filters::DeltaFilter
• changing_seqpos_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• charge : protocols::qsar::scoring_grid::ChargeAtom
• charge_atom_list_ : protocols::qsar::scoring_grid::ChargeGrid
• chbreak_intcpt_ : protocols::abinitio::abscript::AbscriptStageMover
• chbreak_sf_ : protocols::analysis::LoopAnalyzerMover
• chbreak_slope_ : protocols::abinitio::abscript::AbscriptStageMover
• check_alignment_tolerance_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• check_canonicalness_cutoff_ : protocols::features::strand_assembly::SandwichFeatures
• check_fa_dun_ : protocols::match::upstream::BuildSet
• check_frequency_ : protocols::moves::MonteCarlo
• check_MMT_ : protocols::simple_moves::TorsionDOFMover
• check_N_to_C_direction_by_ : protocols::features::strand_assembly::SandwichFeatures
• 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::RNA_LoopCloser
• checkpoint_ : protocols::abinitio::MembraneAbinitio , protocols::forge::remodel::RemodelMover::instruction_flags
• checkpoint_count_ : protocols::boinc::Boinc , protocols::canonical_sampling::MetropolisHastingsMover
• 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_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_DeNovoProtocol
• chemshift_column_ : protocols::abinitio::IterativeBase
• chemshift_overlap_ : protocols::noesy_assign::PeakAssignment
• chemshift_overlap_weight_ : protocols::noesy_assign::PeakAssignmentParameters
• 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_ : 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_chain1_ : protocols::seeded_abinitio::SeedSetupMover
• chi_chain2_ : protocols::seeded_abinitio::SeedSetupMover
• chi_dev_ : protocols::comparative_modeling::Align_RotamerEvaluator
• chi_diff_threshold_ : protocols::dna::PDBOutput
• chi_min_ : protocols::enzdes::EnzdesBaseProtocol
• chi_ranges_ : protocols::make_rot_lib::MakeRotLibOptionsData
• chi_rotamer_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• chi_samplers_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• chi_samples_ : protocols::match::upstream::FullChiSampleSet
• 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
• child_mover_ : protocols::ligand_docking::UnconstrainedTorsionsMover
• children_ : protocols::loop_modeling::LoopMover
• chinum_ : protocols::simple_moves::sidechain_moves::SetChiMover
• chiral_seq_pos_ : protocols::simple_moves::chiral::ChiralMover
• chirality_ : protocols::simple_moves::chiral::ChiralMover
• 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::StepWiseRNA_VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::SWA_MoveSelector
• 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::RNA_ChunkLibrary , protocols::farna::RNA_DeNovoProtocol
• 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::RNA_DeNovoProtocol
• 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::RNA_ChunkLibrary
• chunk_silent_files_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• chunks_ : protocols::frag_picker::FragmentPicker , protocols::frag_picker::VallProvider , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::nonlocal::SingleFragmentMover , protocols::rigid::RigidBodyMotionMover
• chunks_last_ : protocols::hybridization::HybridizeFoldtreeDynamic
• ci_rpes_ : protocols::simple_moves::GreenPacker
• ci_sfxn_ : protocols::simple_moves::GreenPacker
• ciBR_only_ : protocols::pack_daemon::FASTER_IG_Repacker
• cif_files_ : protocols::cryst::SetRefinementOptionsMover
• cis_trans_conf : protocols::antibody::clusters::ClusterData
• 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_ : protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::TryRotamers
• 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_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• clash_threshold_ : protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• clash_wt_ : protocols::simple_filters::SymmetricMotifFilter
• 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
• close_ : protocols::dna::DnaNeighbor
• close_chain_ : protocols::stepwise::screener::PartitionContactScreener
• close_chbrk_ : protocols::abinitio::ClassicAbinitio
• close_loops_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_Minimizer
• close_loops_after_each_move_ : protocols::farna::RNA_DeNovoProtocol
• close_loops_at_end_ : protocols::farna::RNA_DeNovoProtocol
• close_loops_in_last_round_ : protocols::farna::RNA_DeNovoProtocol
• 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_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::CDRPose , protocols::antibody::clusters::ClusterData
• cluster_ : protocols::antibody::clusters::CDRCluster , protocols::forge::remodel::RemodelAccumulator
• cluster_base_ : protocols::cluster::AssignToClustersMover
• 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_manager_ : protocols::antibody::CDRSetOptionsParser
• cluster_matcher_ : protocols::antibody::clusters::CDRClusterSet
• cluster_num_ : protocols::make_rot_lib::RotData
• cluster_radius : protocols::toolbox::ClusterOptions
• cluster_radius_ : protocols::cluster::ClusterBase , 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_switch_ : protocols::forge::remodel::RemodelAccumulator
• clusterer_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• clusterID_map_ : protocols::hybridization::HybridizeProtocol
• 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_ : protocols::simple_filters::HolesFilter
• cmd_line_csts_ : protocols::comparative_modeling::LoopRelaxMover
• cmd_line_operation_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• coarse_angle_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• coarse_rna_ : protocols::farna::RNA_ChunkLibrary
• coarse_rna_name_to_num_ : protocols::coarse_rna::CoarseRNA_Fragments
• coarse_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• coef1_ : protocols::branch_angle::BranchAngleOptimizer
• coef2_ : protocols::branch_angle::BranchAngleOptimizer
• coef_ : protocols::forge::constraints::NtoC_RCG
• coef_map1_ : protocols::branch_angle::BranchAngleOptimizer
• coef_map2_ : protocols::branch_angle::BranchAngleOptimizer
• coeffs_ : protocols::sasa_scores::Poly
• 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 : 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
• 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_size_ : protocols::canonical_sampling::AsyncMPITemperingBase
• command : protocols::relax::RelaxScriptCommand
• command_ : protocols::rpc::JSON_RPC , protocols::simple_filters::ExternalEvaluator
• comment_exists_ : protocols::simple_filters::PoseComment
• comment_name_ : protocols::simple_filters::PoseComment
• comment_value_ : protocols::simple_filters::PoseComment
• COMMIT_LIMIT_BETWEEN_UPDATES : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• communicator_handle_ : protocols::jd2::MPIMultiCommJobDistributor
• comp : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• 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
• 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_id_ : protocols::frag_picker::CompareScoreComponent
• component_weights_ : protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEMultifunc
• components_ : 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_statement_ : protocols::filters::CompoundFilter
• compound_task_ : protocols::toolbox::task_operations::StoreCompoundTaskMover
• 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_packstat_ : protocols::analysis::InterfaceAnalyzerMover , protocols::features::InterfaceFeatures
• compute_rmsd_ : protocols::comparative_modeling::LoopRelaxMover
• compute_separated_sasa_ : protocols::analysis::InterfaceAnalyzerMover
• condist_ : protocols::fldsgn::NcontactsCalculator
• condition_ : protocols::protein_interface_design::movers::LoopOver
• cone_angle_cos_ : protocols::scoring::methods::pcs2::GridSearchIterator , 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_ : protocols::viewer::ConformationViewer
• conf_event_link_ : protocols::boinc::BoincCurrentPoseObserver
• conf_num_ : protocols::docking::DockingEnsemble
• conf_size_ : protocols::docking::DockingEnsemble
• confidence_ : protocols::filters::StochasticFilter
• config_file_ : protocols::topology_broker::TemplateFragmentClaimer
• conformation_ : protocols::environment::DofUnlock
• conformations_for_flexible_segments_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• conformer_group_for_conformer_ : protocols::match::downstream::LigandConformerBuilder
• conformer_group_indices_ : protocols::match::downstream::LigandConformerBuilder
• Conformers : protocols::sparta::PDB
• connect_from_ : protocols::protein_interface_design::movers::SetAtomTree
• connect_to_ : protocols::protein_interface_design::movers::SetAtomTree
• connected_resonance_ids_ : protocols::noesy_assign::Resonance
• connected_resonance_ptrs_ : protocols::noesy_assign::Resonance
• connection_event_link_ : protocols::viewer::ConformationViewer
• connection_id_ : protocols::ligand_docking::AddHydrogen
• 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::antibody::design::ConservativeDesignOperation
• conserved_pos_taskop_ : protocols::simple_filters::ConservedPosMutationFilter
• consolidate_matches_ : protocols::match::MatcherTask
• CONST_SCORE : protocols::frag_picker::scores::ConstScore
• constrain_coords_ : protocols::relax::RelaxProtocolBase
• constrain_cter_ : protocols::antibody::AntibodyModelerProtocol
• constrain_dist_only_ : protocols::fldsgn::SheetConstraintsRCG
• 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_ : protocols::md::MDBase
• constrained_lig_atoms_ : protocols::enzdes::EnzdesConstraintReporter
• constrained_nonligand_atoms_ : protocols::enzdes::EnzdesConstraintReporter
• 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_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• 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
• constraint_weights_ : protocols::enzdes::EnzdesBaseProtocol
• constraints_ : 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_NtoC_ : protocols::fldsgn::BluePrintBDR , protocols::flxbb::FlxbbDesign
• constraints_only_ : protocols::idealize::IdealizeMover
• 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::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_dist_cutoff_squared_ : protocols::frag_picker::FragmentPicker
• contacts_dist_cutoffs_squared_ : protocols::frag_picker::FragmentPicker
• contacts_min_seq_sep_ : protocols::frag_picker::FragmentPicker
• contents_ : protocols::checkpoint::FileBuffer
• 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
• controlling_chi_for_atom_ : protocols::match::upstream::UpstreamResTypeGeometry
• convergence_checks_ : protocols::moves::MonteCarlo
• convert_scores_to_probabilities_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• coor_cst_cutoff_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• Coord : protocols::sparta::CORdata
• coord_constrain_sidechains_ : protocols::relax::RelaxProtocolBase
• coord_cst_func_ : protocols::protein_interface_design::movers::PlaceStubMover
• coord_cst_std_ : protocols::protein_interface_design::movers::PlaceStubMover
• coord_cst_weight_ : protocols::farna::RNA_Minimizer
• coord_dev_ : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• coord_dev_factor_ : protocols::electron_density::DensityMorphingMover
• coord_sdev_ : protocols::farna::RNA_Minimizer , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• coordA : protocols::sparta::RingData
• coordinate_cacher_ : protocols::match::output::PDBWriter , protocols::match::output::WriteKinemageOutputter
• coordinate_constraint_weight_ : protocols::abinitio::LoopJumpFoldCst , protocols::idealize::IdealizeMover
• coordinate_constraint_weights_ : protocols::abinitio::LoopJumpFoldCst
• coordinates : protocols::pockets::SmallMol
• coords_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , protocols::match::downstream::TargetRotamerCoords , protocols::match::output::UpstreamDownstreamCollisionFilter , 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_ : 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
• 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_chunks_last_ : protocols::hybridization::HybridizeFoldtreeDynamic
• core_cutoff_ : protocols::toolbox::pose_metric_calculators::SequenceComparison
• 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
• cost_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::simple_moves::SmoothFragmentMover
• count : protocols::make_rot_lib::running_average_pair
• count_ : 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
• 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
• cov_bond_only_flag_ : protocols::ub_e2c::ubi_e2c_modeler
• 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::RNA_ChunkLibrary
• 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
• 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
• crossing_angle : protocols::features::helixAssembly::FragmentPair
• crosspeak_ : protocols::noesy_assign::PeakAssignment
• crosspeaks_ : protocols::noesy_assign::NoesyModule
• crossterm_interface_energy : protocols::analysis::InterfaceData
• crossterm_interface_energy_dSASA_ratio : protocols::analysis::InterfaceData
• csa_bank_size_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• csa_rmsd_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• csequence_ : protocols::seeded_abinitio::GrowPeptides
• 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_ : 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::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_io_ : protocols::match::output::OutputWriter
• cst_jumps_ : protocols::jumping::ResiduePairJump
• cst_lib_ : protocols::constraints_additional::CombinedConstraintEvaluator
• cst_map_ : protocols::forge::remodel::RemodelConstraintGenerator
• 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_sd_ : protocols::relax::AtomCoordinateCstMover
• cst_sdev_ : protocols::md::MDBase , protocols::normalmode::NormalModeRelaxMover
• cst_seqwidth_ : protocols::rbsegment_relax::RBSegmentRelax
• cst_set_ : protocols::ddg::ddGMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::StepWiseModeler
• cst_sidechain_ : protocols::relax::AtomCoordinateCstMover
• cst_source_ : protocols::constraints_additional::ConstraintEvaluator
• cst_stdev_ : protocols::rbsegment_relax::RBSegmentRelax
• cst_strength_ : protocols::noesy_assign::PeakAssignmentParameters
• cst_type_ : protocols::protein_interface_design::movers::TaskAwareCsts
• cst_weight : protocols::simple_moves::ShakeStructureMover
• cst_weight_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::docking::DockingProtocol , protocols::electron_density::DensityMorphingMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::RBSegmentRelax , 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::forge::remodel::RemodelConstraintGenerator , protocols::sic_dock::ConstraintSetScore
• 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
• 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::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_length_ : protocols::match::RemoveNorCTermMPM
• cterm_rsd_num_ : protocols::simple_moves::CyclizationMover
• cube_dim_ : protocols::scoring::ImplicitFastClashCheck
• cube_dim_ca_ : protocols::scoring::ImplicitFastClashCheck
• 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_replicas_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulated_jobs_ : protocols::jd2::MPIFileBufJobDistributor
• cumulated_runtime_ : protocols::jd2::MPIFileBufJobDistributor
• 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::BundleGridSamplerHelper
• cur_ncluster_ : protocols::toolbox::KMedoid
• curr_bin_ : protocols::match::VoxelSetIterator
• curr_coordinate_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover
• curr_exemplar : protocols::cluster::DataPoint
• curr_gen_entities_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• curr_idx_ : protocols::inputter::FastaInputter , protocols::inputter::PDBInputter , protocols::inputter::SilentFileInputter
• curr_jobid_ : protocols::jobdist::BaseJobDistributor
• curr_loop_end_ : protocols::protein_interface_design::movers::PlaceOnLoop
• 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_score_log : protocols::relax::SRelaxPose
• curr_state_ : protocols::stepwise::sampler::StepWiseSamplerSizedAny
• curr_state_one_body_energy_ : protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_total_energy_ : protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_two_body_energies_ : 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_end : protocols::antibody_legacy::Antibody
• current_energy_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• current_exchange_schedule_ : protocols::canonical_sampling::HamiltonianExchange
• 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_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_mem_ : protocols::wum2::WUQueue
• current_mode_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• current_noesy_sampling_file_ : protocols::abinitio::IterativeBase
• current_nstruct_ : protocols::jd2::MSDJobDistributor , protocols::jobdist::BaseJobDistributor
• current_ntrial_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• 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_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_radial_disps_ : protocols::matdes::SymDofMoverSampler
• current_receptor_chain_letter_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverPoseOutputter
• current_rigid_core_ : protocols::topology_broker::RigidChunkClaimer
• 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_ : protocols::flexpack::interaction_graph::FlexbbNode
• current_state_info_ : protocols::flexpack::interaction_graph::FlexbbNode
• current_struct : protocols::relax::SRelaxPose
• 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_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_structure_input_tag_ : protocols::features::ReportToDB
• custom_structure_tag_ : protocols::features::ReportToDB
• 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_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
• cutoff_ : 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_distance_ : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• cutoff_flag_ : protocols::match::downstream::ScoringSecMatchRPE
• cutoff_scoreType_flag_ : protocols::match::downstream::ScoringSecMatchRPE
• cutoff_squared_ : protocols::frag_picker::SidechainContactDistCutoff
• cutoffE_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• cutpoint_ : protocols::antibody::H3RefineCCD , protocols::simple_moves::ChainSplitMover
• cutpoint_closed_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• cutpoint_closed_list_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• 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::RNA_StructureParameters
• cutpoints_open_ : protocols::farna::RNA_StructureParameters
• 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
• 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_ : protocols::abinitio::abscript::AbscriptStageMover , protocols::grafting::AnchoredGraftMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::movers::LoopRemodel , protocols::rbsegment_relax::RBSegmentRelax , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• cycles_adjust_ : protocols::abinitio::abscript::AbscriptStageMover
• cycles_inner_ : protocols::dna::DesignProteinBackboneAroundDNA
• cycles_outer_ : protocols::dna::DesignProteinBackboneAroundDNA