- a -

• a : protocols::md::Constraint , protocols::pockets::UnionEdge , protocols::sic_dock::Vec3
• A_ : protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• a_ : 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
• A_all_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• a_axis_ : protocols::docking::EllipsoidalRandomizationMover
• a_form_range_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• a_form_torsions_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• a_ids_ : protocols::scoring::methods::saxs::PDDFEnergy
• a_ik : protocols::cluster::Exemplar
• A_index_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• a_kk : protocols::cluster::DataPoint
• a_little_verbose_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• a_to_i_ : protocols::normalmode::NormalMode
• aa : protocols::forge::remodel::RemodelWorkingSet
• aa1 : protocols::farna::BasePairType
• aa2 : protocols::farna::BasePairType
• aa_ : protocols::forge::build::Bridge , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::frag_picker::VallResidue , protocols::jd2::parser::FragmentReader , protocols::noesy_assign::MethylNames , protocols::noesy_assign::Resonance , protocols::optimize_weights::PNatRotOptEPositionData
• AA_ : protocols::protein_interface_design::movers::BuildAlaPose
• aa_ : protocols::simple_moves::MakePolyXMover
• aa_during_build : protocols::forge::components::BDRSegmentInfo
• aa_during_design_refine : protocols::forge::components::BDRSegmentInfo
• aa_exp_ : protocols::optimize_weights::IterativeOptEDriver
• aa_freq_exp_ : protocols::optimize_weights::IterativeOptEDriver
• aa_freq_obs_ : protocols::optimize_weights::IterativeOptEDriver
• aa_map_ : protocols::frag_picker::SidechainContactDistCutoff
• AA_name3_ : protocols::simple_moves::ResidueTypeConstraintMover
• aa_obs_ : protocols::optimize_weights::IterativeOptEDriver
• aa_order_map_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• aa_sets_dec_line_ : protocols::pack_daemon::EntityFunc
• aa_sets_name_map_ : protocols::pack_daemon::EntityFunc
• aa_to_index_map_ : protocols::frag_picker::SidechainContactDistCutoff
• AAlist : protocols::sparta::Sparta::SpartaLib
• ab_dock_chains_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• ab_fold_tree_ : protocols::protein_interface_design::movers::SetAtomTree
• ab_info_ : protocols::antibody::AntibodyDatabaseManager , protocols::antibody::AntibodyFeatures , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::clusters::CDRClusterSet , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover , protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop
• ab_manager_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• ab_movemap : protocols::antibody_legacy::Antibody
• ab_sequence_ : protocols::antibody::AntibodyInfo
• ab_t_info_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftOneCDRLoop
• abego : protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelWorkingSet
• abego_ : protocols::forge::components::VarLengthBuild , protocols::jd2::parser::BluePrint
• abinitio_ : protocols::surface_docking::SurfaceDockingProtocol
• abinitio_mover_weight_ : protocols::topology_broker::TopologyClaimer
• abort_on_failed_loop_ : protocols::LoopRebuild
• abrelax_checkpoints_ : protocols::abinitio::AbrelaxApplication
• absolute_ccd_tolerance_ : protocols::farna::RNA_LoopCloser
• absX : protocols::pockets::CCluster::Cxyz
• absY : protocols::pockets::CCluster::Cxyz
• absZ : protocols::pockets::CCluster::Cxyz
• acc_ : protocols::md::MDBase
• acc_dist_cutoff_ : protocols::features::WaterFeatures
• accept_aborted_loops_ : protocols::loops::loop_mover::IndependentLoopMover
• accept_according_to_dunbrack_ : protocols::simple_moves::sidechain_moves::SidechainMover
• accept_blocks_missing_header_ : protocols::enzdes::AddOrRemoveMatchCsts
• accept_count : protocols::relax::SRelaxPose
• accept_counter_ : protocols::moves::TrialCounter , protocols::simple_moves::GenericMonteCarloMover
• accept_hists_ : protocols::backrub::BackrubSidechainMover
• accept_rate_ : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• acceptance_history_ : protocols::jd2::archive::ArchiveBase
• accepted_ : protocols::moves::MoverStatistics
• acceptorList : protocols::sparta::PDB
• acceptors : protocols::sic_dock::EdgeStandScore
• acceptors_ : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• accepts_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• accepts_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• accumulated_count_ : protocols::noesy_assign::PeakCalibrator
• accumulated_target_ : protocols::noesy_assign::PeakCalibrator
• accumulator_ : protocols::forge::remodel::RemodelMover
• acid_base_ : protocols::simple_moves::IonizableResidue
• action_ : protocols::loophash::EXCN_DB_IO_Failed
• activated_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• active : protocols::relax::SRelaxPose
• active_ : protocols::optimize_weights::WeightRangeConstraint
• active_angle_ : protocols::stepwise::sampler::MC_OneTorsion
• active_constraints_ : protocols::constraints_additional::AmbiguousMultiConstraint
• active_peaks_ : protocols::noesy_assign::DistanceScoreMover
• active_pose_constraints_ : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• active_pucker_state_ : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• active_sequence_labels_ : protocols::topology_broker::FragmentClaimer
• active_site_grid_ : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::Matcher
• active_variables_ : protocols::optimize_weights::WrapperOptEMultifunc
• active_variables_this_dependent_dof_ : protocols::optimize_weights::WrapperOptEMultifunc
• activity : protocols::qsar::qsarOptData
• actual_cycles_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• actual_phosphate_move_list_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• actual_rep_cutoff_ : protocols::stepwise::screener::PartitionContactScreener
• adapt_graft_ : protocols::antibody::design::AntibodyGraftDesignMover
• adaptation_period_ : protocols::simple_moves::GenericMonteCarloMover
• adaptive_ : protocols::simple_moves::GenericMonteCarloMover
• adaptive_movers_ : protocols::simple_moves::GenericMonteCarloMover
• add_base_pair_constraints_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• add_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::CyclizationMover
• add_cst_seed_ : protocols::seeded_abinitio::CAcstGenerator
• add_delete_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• add_fuzzy_ : protocols::abinitio::HedgeArchive
• add_helix_capping_ : protocols::flxbb::LayerDesignOperation
• add_hetatm_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• add_lead_zero_to_tag_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• add_ligand_to_pose_ : protocols::forge::constraints::InvrotTreeRCG
• add_membrane_mover_ : protocols::docking::membrane::MPDockingMover
• add_mover_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• add_nbr_radius_ : protocols::ligand_docking::LigandArea
• add_non_init_chunks_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• add_observer_cache_segs_to_interface_ : protocols::enzdes::DetectProteinLigandInterface
• add_or_delete_mover_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• add_peptide_plane_variants_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• add_target_ : protocols::seeded_abinitio::SeedFoldTree
• add_target_to_pose_ : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• add_target_types_ : protocols::simple_moves::ModifyVariantTypeMover
• add_termini_ : protocols::cyclic_peptide::DeclareBond
• add_to_allowed_aas_ : protocols::antibody::design::ConservativeDesignOperation
• add_virt_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• add_virt_res_as_root_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• add_virtual_anchor_ : protocols::farna::RNA_StructureParameters
• added_cutpoint_closed_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• addition_type_ : protocols::simple_moves::HelicalPeptideLengthMover
• additional_low_resolution_steps_ : protocols::docking::DockingProtocol
• additional_task_operations_ : protocols::docking::DockTaskFactory
• address_ : protocols::canonical_sampling::mc_convergence_checks::PoolData
• addtime_ : protocols::simple_moves::DumpPdb
• ADJ_Tab : protocols::sparta::Sparta::SpartaLib
• adjFileName : protocols::sparta::Sparta::SpartaLib
• adp_strategy_ : protocols::cryst::FitBfactorsMover
• ads_sec_struct_ : protocols::surface_docking::FullatomRelaxMover
• after_minimization_reference_energies_ : protocols::optimize_weights::IterativeOptEDriver
• after_placement_filter_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• ag_ab_atomic_contacts_ : protocols::antibody::AntibodyFeatures
• aggregate_ : protocols::pack_daemon::MultistateFitnessFunction
• aggregate_function_ : protocols::multistate_design::MultiStateFitnessFunction
• ahd_cutoff_ : protocols::features::WaterFeatures
• akash_dyepos_ : protocols::anchored_design::AnchorMoversData
• algo_ : protocols::cryst::SetRefinementOptionsMover
• algorithm_ : protocols::loops::loop_mover::LoopCM , protocols::match::upstream::BuildSet
• algorithm_inputs_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• align_ : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::protein_interface_design::movers::TopologyBrokerMover
• align_angle_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::topology::HelixPairing
• align_chunk_ : protocols::hybridization::ChunkTrialMover
• align_domains_to_pose_ : protocols::hybridization::HybridizeSetup
• align_domains_to_template_ : protocols::hybridization::HybridizeSetup
• align_file_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• align_idx_ : protocols::id::AlignmentID
• align_input_axes_to_symdof_axes_ : protocols::matdes::SymDofMover
• align_only_over_base_atoms_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• align_option_ : protocols::hybridization::ChunkTrialMover
• align_set_ : protocols::comparative_modeling::AlignmentSet
• align_templates_to_pose_ : protocols::hybridization::CartesianHybridize
• align_to_native_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• align_to_pdbname_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• align_to_ss_only_ : protocols::hybridization::InsertChunkMover
• align_torsions_ : protocols::farna::FragmentLibrary
• align_trial_counter_ : protocols::hybridization::InsertChunkMover
• aligned_ : protocols::star::Extender
• alignment_ : protocols::comparative_modeling::ThreadingJob , protocols::simple_filters::RelativePoseFilter , protocols::star::Extender
• alignment_atom_id_map_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• alignment_file_ : protocols::toolbox::task_operations::AlignedThreadOperation
• alignment_res_string_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• alignments_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingJobInputter
• all_abego_ : protocols::frag_picker::quota::ABEGO_SS_Map , protocols::frag_picker::quota::ABEGO_SS_Pool
• all_ala_C : protocols::seeded_abinitio::GrowPeptides
• all_ala_N : protocols::seeded_abinitio::GrowPeptides
• all_atom_inds_ : protocols::match::output::SingleDownstreamResidueWriter
• all_atom_mode_ : protocols::ligand_docking::LigandArea
• all_atom_residue_depth_ : protocols::frag_picker::VallResidue
• all_bfactors_zero_ : protocols::match::BfactorMPM
• all_boltz_ : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• all_build_points_ : protocols::match::Matcher
• all_bur_unsat_polars_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• all_cdr_loops : protocols::antibody_legacy::Antibody
• all_dist_buf_ : protocols::noesy_assign::DistanceScoreMover
• all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• all_downstream_algorithms_ : protocols::match::Matcher
• all_downstream_builders_ : protocols::match::Matcher
• all_energies_ : protocols::toolbox::DecoySetEvaluation
• all_frames_ : protocols::topology_broker::DisulfJumpClaimer
• all_gap_ : protocols::toolbox::task_operations::CrystalContactsOperation
• all_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• all_hits_ : protocols::match::HitNeighborFinder
• all_invrots_ : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• all_jump_pairings_ : protocols::topology_broker::DisulfJumpClaimer
• all_lex_states : protocols::match::MatcherOutputStats
• all_loops_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy
• all_loops_closed_ : protocols::loops::loop_mover::IndependentLoopMover
• all_lores_score_final_ : protocols::farna::RNA_DeNovoProtocol
• all_movable_ : protocols::seeded_abinitio::SegmentHybridizer
• all_mutants_ : protocols::pmut_scan::PointMutScanDriver
• all_pairings_ : protocols::jumping::DisulfPairingLibrary
• all_pose_to_output_pose_ID_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• all_pssm_data_ : protocols::optimize_weights::IterativeOptEDriver
• all_rigid_body_settings_save_ : protocols::stepwise::legacy::modeler::RigidBodySampler
• all_rna_fragments_ : protocols::farna::RNA_DeNovoProtocol
• all_rna_fragments_file_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• all_seeds_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SwapSegment
• all_ss_ : protocols::frag_picker::quota::ABEGO_SS_Map , protocols::frag_picker::quota::ABEGO_SS_Pool
• all_structs_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• all_target_res_ : protocols::toolbox::match_enzdes_util::InvrotTarget
• all_unsat_polars_ : protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• all_vs_bb_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• all_vs_bb_energy_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• all_vs_bb_energy_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• allcdr_map_ : protocols::antibody::CDRsMinPackMin
• allGroups_ : protocols::toolbox::task_operations::LinkResidues
• allow_all_aas_ : protocols::seeded_abinitio::SeedSetupMover , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• allow_anchor_repack_ : protocols::anchored_design::AnchorMoversData
• allow_base_pair_only_centroid_screen_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_base_pair_only_screen_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• allow_bondangles_ : protocols::helical_bundle::parameters::BundleParameters
• allow_bondlengths_ : protocols::helical_bundle::parameters::BundleParameters
• allow_bulge_ : protocols::farna::RNA_DeNovoProtocol
• allow_bulge_at_chainbreak_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_chain_boundary_jump_partner_right_at_fixed_BP_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• allow_chi_copy_ : protocols::simple_moves::ReturnSidechainMover
• allow_chi_during_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• allow_consecutive_bulges_ : protocols::farna::RNA_DeNovoProtocol
• allow_cuts_inside_base_pair_steps_ : protocols::farna::RNA_StructureParameters
• allow_delete_ : protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_design_ : protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• allow_design_around_ : protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::ThreadSequenceOperation
• allow_dihedrals_ : protocols::helical_bundle::parameters::BundleParameters
• allow_duplicates : protocols::environment::claims::ResidueElement
• allow_fixed_res_at_moving_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• allow_insert_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::farna::RNA_ChunkLibrary , protocols::farna::RNA_FragmentMover , protocols::farna::RNA_Minimizer , protocols::farna::RNA_StructureParameters , protocols::simple_moves::ConstrainToIdealMover , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::StepWiseMinimizer , protocols::toolbox::AllowInsert
• allow_insert_res_ : protocols::farna::RNA_StructureParameters
• allow_internal_hinge_ : protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_internal_hinge_moves_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_internal_local_ : protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_internal_local_moves_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_overlap_ : protocols::ligand_docking::CompoundTranslate
• allow_reading_cancelled_decoys_ : protocols::jd2::archive::Batch
• allow_repack_ : protocols::antibody::H3RefineCCD
• allow_repacking_ : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• allow_shared_chains_in_dock_poses_ : protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_skip_bulge_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_split_off_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_syn_pyrimidine_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_variable_bond_geometry_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• allow_virtual_o2prime_hydrogens_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_virtual_side_chains_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allowed_aas_ : protocols::simple_moves::DesignRepackMover
• allowed_aas_per_jump_ : protocols::protein_interface_design::movers::MapHotspot
• allowed_bulge_res_ : protocols::farna::RNA_DeNovoProtocol
• allowed_closure_attempts_ : protocols::forge::remodel::RemodelLoopMover
• allowed_deviation_for_turn_type_id_ : protocols::features::strand_assembly::SandwichFeatures
• allowed_failure_before_extend_ : protocols::LoopRebuild
• allowed_failure_before_stop : protocols::LoopRebuild
• allowed_failure_before_stop_ : protocols::LoopRebuild
• allowed_positions_ : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• allowed_res_types_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_res_types_pointers_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_separation_ : protocols::antibody::CloseOneCDRLoop , protocols::antibody_legacy::CloseOneMover
• allowed_seqpos_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_to_move_ : protocols::hybridization::HybridizeProtocol
• allowed_types_ : protocols::dna::DnaInterfacePacker , protocols::motifs::BuildPosition
• allowSeqShiftMoves_ : protocols::rbsegment_relax::AutoRBMover
• AllowSlideJumpMap_ : protocols::simple_moves::symmetry::SymmetrySlider
• allowSSFragInserts_ : protocols::rbsegment_relax::AutoRBMover
• allprotein_tf_ : protocols::flexpep_docking::FlexPepDockingProtocol
• allsc_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• aln_ : protocols::comparative_modeling::Align_RotamerEvaluator , protocols::evaluation::AlignEvaluator , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• alns : protocols::comparative_modeling::AlignmentCluster
• alns_ : protocols::jd2::InnerMultiThreadingJob
• alpha : protocols::protein_interface_design::Transformation , Transformation
• alpha_ : protocols::dna::DNABase , protocols::rigid::WholeBodyRotationMover , protocols::simple_moves::UniformRotationMover , protocols::stepwise::legacy::modeler::RigidBodySampler , protocols::stepwise::sampler::rigid_body::EulerAngles
• alpha_increment_ : protocols::stepwise::legacy::modeler::RigidBodySampler
• alpha_max_ : protocols::stepwise::legacy::modeler::RigidBodySampler
• alpha_min_ : protocols::stepwise::legacy::modeler::RigidBodySampler
• already_moved_ : protocols::simple_moves::BackboneMover
• already_virtualized_res_list_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• alt_e_up_to_date_ : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_energy_ : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_rot_inds_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alt_rots_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alternate_pose_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alternate_pose_energy_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alternate_state_ : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_info_ : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_is_being_considered_ : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_one_body_energy_ : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_total_energy_ : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_two_body_energies_ : protocols::flexpack::interaction_graph::FlexbbNode
• altitude_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• altitude_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• altitude_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• amb_hnq_ : protocols::relax::AtomCoordinateCstMover
• aminoAcidList : protocols::forge::remodel::LineObject
• amplitude_ : protocols::dna::DNABase
• aN : protocols::sparta::Sparta::SpartaLib
• aname1_ : protocols::enzdes::DiffAtomSasaFilter
• aname2_ : protocols::enzdes::DiffAtomSasaFilter
• anchor_ : protocols::anchored_design::AnchorMoversData
• anchor_atom_dest_ : protocols::comparative_modeling::StealLigandMover
• anchor_atom_id_ : protocols::seeded_abinitio::CoordinateCst
• anchor_atom_source_ : protocols::comparative_modeling::StealLigandMover
• anchor_chain_ : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer
• anchor_id_ : protocols::viewer::ConformationViewer
• anchor_insert_only_ : protocols::hybridization::InsertChunkMover
• anchor_loop_index_ : protocols::anchored_design::AnchorMoversData
• anchor_noise_constraints_mode_ : protocols::anchored_design::AnchorMoversData
• anchor_offset_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::multistate_design::PartitionAggregateFunction< T > , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• anchor_positions_ : protocols::hybridization::HybridizeFoldtreeDynamic
• anchor_positions_last_ : protocols::hybridization::HybridizeFoldtreeDynamic
• anchor_res_ : protocols::protein_interface_design::movers::SetAtomTree , protocols::seeded_abinitio::CoordinateCst
• anchor_reses_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• anchor_residue_ : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer
• anchor_residues_ : protocols::hybridization::AllResiduesChanged
• anchor_resnum_ : protocols::protein_interface_design::movers::TaskAwareCsts
• anchor_specified_ : protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• anchor_sugar_modeling_ : protocols::stepwise::screener::AnchorSugarScreener
• anchor_sugar_solution_number_ : protocols::stepwise::screener::AnchorSugarScreener
• anchor_via_constraints_ : protocols::anchored_design::AnchorMoversData
• anchored_graft_mover_ : protocols::antibody::design::AntibodyGraftDesignMover
• anchorfile_ : protocols::anchored_design::Anchor
• anchors_ : protocols::protein_interface_design::filters::BoltzmannFilter , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• ang123_ : protocols::toolbox::match_enzdes_util::LigandConformer
• ang_D1D2D3_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U1D2_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• ang_U1D2_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U2D1_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• ang_U2D1_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• angle : protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral , protocols::ligand_docking::Transform_info , protocols::make_rot_lib::CentroidRotNum
• angle_ : protocols::matdes::GetRBDOFValues , protocols::membrane::FlipMover , protocols::rigid::RollMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::SetChiMover
• angle_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• angle_deltas_ : protocols::matdes::SymDofMover
• angle_disp_ : protocols::backrub::BackrubSegment
• angle_magnitude_ : protocols::rigid::RigidBodyDeterministicSpinMover
• angle_max_ : protocols::simple_moves::BackboneMover , protocols::stepwise::sampler::MC_OneTorsion , protocols::surface_docking::FullatomRelaxMover
• angle_min_ : protocols::stepwise::sampler::MC_OneTorsion
• angle_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• angle_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• angle_steps_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• angle_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• angle_tolerance_ : protocols::fldsgn::SheetConstraintsRCG
• angle_wt_ : protocols::simple_filters::SymmetricMotifFilter
• angle_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• angleA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• angleB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• anglelist : protocols::cartesian::MolecularDynamics
• angles : protocols::loophash::BBData
• angles_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler , protocols::pockets::PocketConstraint
• angles_range_max_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• angles_range_min_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• angstroms : protocols::ligand_docking::Translate_info
• angstroms_ : protocols::ligand_docking::TetherLigand
• angth : protocols::kinmatch::KRSQuery
• animate_ : protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• ann : protocols::environment::EnvClaimBroker::BrokerResult
• ann_ : protocols::environment::EnvClaimBroker , protocols::environment::Environment
• ANN_CS_OUTPUT_FULL : protocols::sparta::Sparta::SpartaLib
• ANN_IN_MTX : protocols::sparta::ANN , protocols::sparta::Sparta::SpartaLib
• ANN_IN_MTX_LEVEL1 : protocols::sparta::ANN
• ANN_IN_MTX_LEVEL2 : protocols::sparta::ANN
• ANN_OUT_MTX_LEVEL1 : protocols::sparta::ANN
• ANN_OUT_MTX_LEVEL2 : protocols::sparta::ANN
• annotated_sequence_ : protocols::topology_broker::claims::SequenceClaim
• annotated_sequence_used_for_atom_id_maps_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• annotations_ : protocols::environment::ProtectedConformation
• anti_ : protocols::abinitio::AlternativePairings
• antibody_build_ : protocols::antibody_legacy::CDRH3Modeler
• antibody_in_ : protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler
• antibody_info_ : protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol
• antibody_refine_ : protocols::antibody_legacy::CDRH3Modeler
• antibody_region_to_enum_ : protocols::antibody::AntibodyEnumManager
• antibody_region_to_string_ : protocols::antibody::AntibodyEnumManager
• antigen_chains_ : protocols::antibody::constraints::ParatopeSiteConstraintMover
• APBS_CONFIG_EXT : protocols::pb_potential::SetupPoissonBoltzmannPotential
• APBS_DX_EXT : protocols::pb_potential::SetupPoissonBoltzmannPotential
• APBS_PQR_EXT : protocols::pb_potential::SetupPoissonBoltzmannPotential
• append_n_residues_ : protocols::ncbb::oop::OopCreatorMover
• applied_fullatom_pert_ : protocols::ub_e2c::ubi_e2c_modeler
• apply_ambiguous_constraints_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• apply_centroid_mode_ : protocols::antibody_legacy::CDRH3Modeler
• apply_fullatom_mode_ : protocols::antibody_legacy::CDRH3Modeler
• apply_large_frags_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• apply_probability_ : protocols::rosetta_scripts::ParsedProtocol
• apply_residue_alternative_sampler_ : protocols::stepwise::screener::SampleApplier
• apply_self_energies_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• apply_to_centroid_ : protocols::abinitio::ResolutionSwitcher
• apply_vdw_cut_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• apply_virtual_res_variant_at_dinucleotide_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• approved_ : protocols::topology_broker::claims::DofClaim
• arc_ : protocols::jd2::archive::SortPredicate
• archive_rank_ : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor
• archived_starting_task_ : protocols::forge::remodel::RemodelDesignMover
• arg_sweep_cutoff_ : protocols::enzdes::DetectProteinLigandInterface
• arg_sweep_interface_ : protocols::enzdes::DetectProteinLigandInterface
• argc_ : protocols::rpc::BasicCmdLineInit
• argv_ : protocols::rpc::BasicCmdLineInit
• aromatic_dG_fraction : protocols::analysis::InterfaceData
• aromatic_dSASA_fraction : protocols::analysis::InterfaceData
• aromatic_motifs_ : protocols::motifs::MotifDnaPacker
• aromatic_nres : protocols::analysis::InterfaceData
• around_shell_ : protocols::simple_filters::EnergyPerResidueFilter
• assert_jump_point_in_fixed_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• assign_new_cluster_tag : protocols::toolbox::ClusterOptions
• assign_WC_edges_ : protocols::stepwise::legacy::modeler::RigidBodySampler
• assigned_num_ : protocols::loophash::LoopHashLibrary
• assigned_string_ : protocols::loophash::LoopHashLibrary
• assignment_ : protocols::noesy_assign::EXCN_AssignmentNotFound
• assignments_ : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::CrossPeakList
• assume_atom_ids_invariant_ : protocols::stepwise::modeler::align::StepWiseClusterer
• assume_non_stem_is_loop : protocols::farna::RNA_StructureParameters
• astype1_ : protocols::simple_filters::AtomicDistanceFilter
• astype2_ : protocols::simple_filters::AtomicDistanceFilter
• asymm_only_ : protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• asymmetric_res_ : protocols::topology_broker::SymmetryClaimer
• at1_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at2_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at3_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at_inds_ : protocols::match::downstream::AtomGeometrySecMatchRPE
• atms_ : protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint
• atom1 : protocols::environment::claims::JumpElement
• atom1_ : protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::topology_broker::claims::JumpClaim
• atom2 : protocols::environment::claims::JumpElement
• atom2_ : protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::topology_broker::claims::JumpClaim
• atom2rdc_map_ : protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• atom3_ : protocols::cyclic_peptide::CreateTorsionConstraint , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms
• atom4_ : protocols::cyclic_peptide::CreateTorsionConstraint , protocols::simple_moves::TorsionDOFMover
• atom_ : protocols::noesy_assign::EXCN_UnknownResonance , protocols::noesy_assign::Resonance
• atom_atom_distance : protocols::ligand_docking::rdf::AtomPairData
• atom_atom_overlap_dist_cutoff_ : protocols::stepwise::screener::ResidueContactScreener
• atom_bin_size_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• atom_bur_unsat_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• atom_center_ : protocols::cyclic_peptide::CreateAngleConstraint
• atom_dependent_calibration_ : protocols::noesy_assign::PeakAssignmentParameters
• atom_equiv_ : protocols::comparative_modeling::ThreadingMover
• atom_flags_ : protocols::frag_picker::scores::AtomBasedConstraintsScore
• atom_geom_rpes_ : protocols::match::downstream::GeometrySecMatchRPE
• atom_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• atom_hydrophobic_ : protocols::fldsgn::MyAtom
• atom_id : protocols::cartesian::CartesianAtom
• atom_id_ : protocols::seeded_abinitio::CoordinateCst
• atom_id_1 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• atom_id_2 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• atom_id_3 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral
• atom_id_4 : protocols::cartesian::MD_HarmonicDihedral
• atom_id_mask_ : protocols::farna::ChunkSet
• atom_ids_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::pockets::PocketConstraint , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• atom_ids_for_coordinates_ : protocols::match::downstream::TargetRotamerCoords
• atom_ids_in_res_ : protocols::toolbox::AllowInsert
• atom_index_to_relevant_atom_index_ : protocols::features::AtomAtomPairFeatures
• atom_indices_ : protocols::electron_density::BfactorMultifunc
• atom_inds_for_restype_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_limit_ : protocols::ligand_docking::AtomCountFilter
• atom_map_ : protocols::hybridization::InsertChunkMover , protocols::qsar::qsarMap
• atom_name1_ : protocols::farna::RNA_PairingTemplate
• atom_name2_ : protocols::farna::RNA_PairingTemplate
• atom_name_ : protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::qsar::qsarPoint , protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• atom_pair_constraint_contact_map_ : protocols::frag_picker::FragmentPicker
• atom_pair_constraint_weight_ : protocols::idealize::IdealizeMover
• atom_radii_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::upstream::BuildSet
• atom_required_in_active_site_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom_semiexpl_score_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• atom_tree_diff_ : protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::AtomTreeDiffJobOutputter
• atom_tree_minimizer_ : protocols::stepwise::modeler::StepWiseMinimizer
• atom_type : protocols::pockets::CCluster::Cxyz
• atom_type_dbio_ : protocols::features::AtomTypesFeatures
• atom_unsat_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• atom_vdw_ : protocols::scoring::InterchainPotential
• atomdesg1_ : protocols::simple_filters::AtomicDistanceFilter
• atomdesg2_ : protocols::simple_filters::AtomicDistanceFilter
• atomdesg_ : protocols::protein_interface_design::filters::HbondsToAtomFilter
• atomID_ : protocols::normalmode::NormalMode
• atomlist_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• atomName : protocols::sparta::CORdata
• atomname_ : protocols::contact_map::ContactPartner
• atomNo : protocols::sparta::RingData
• atomno_ : protocols::scoring::ImplicitFastClashCheck
• atomNum : protocols::sparta::CORdata
• atoms : protocols::environment::EnvClaimBroker::BrokeredJumpData
• ATOMS : protocols::sparta::PDB
• atoms : protocols::sparta::RingData
• atoms_ : protocols::environment::claims::JumpClaim , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• atoms_123_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atoms_downstream_ : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• atoms_in_patches_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• atoms_to_atoms_ : protocols::toolbox::task_operations::CrystalContactsOperation
• atoms_to_compare_ : protocols::match::output::DownstreamRMSEvaluator
• atoms_to_superimpose_on_ : protocols::enzdes::EnzdesBaseProtocol
• atoms_upstream_ : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• AtomSurfaceFullList : protocols::sparta::PDB
• AtomSurfacePartList : protocols::sparta::PDB
• atr : protocols::ligand_docking::Ligand_info
• atr_cutoff_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::screener::PartitionContactScreener
• atr_radius_ : protocols::qsar::scoring_grid::ClassicGrid
• atr_rep_check_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMultiPosePacker
• atr_rep_checker_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMultiPosePacker , protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::legacy::screener::ProteinAtrRepScreener , protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::BulgeApplier
• atr_rep_checker_with_instantiated_sugar_ : protocols::stepwise::screener::AnchorSugarScreener
• atr_rep_checkers_for_anchor_sugar_models_ : protocols::stepwise::screener::AnchorSugarScreener
• atr_rep_screen_ : protocols::stepwise::options::StepWiseBasicOptions
• atr_rep_screening_pose_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler
• atr_rep_screening_scorefxn_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• ats123_reqd_in_active_site_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• attached_res_ : protocols::stepwise::monte_carlo::Attachment
• attachment_type_ : protocols::stepwise::monte_carlo::Attachment
• attachments_ : protocols::stepwise::monte_carlo::SWA_Move
• attempt_closure_cutoff_ : protocols::farna::RNA_LoopCloser
• auction_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• auction_results_ : protocols::protein_interface_design::movers::PlacementAuctionMover
• auto_adjust_factorA_ : protocols::simple_moves::BBGaussianMover
• auto_cuts : protocols::environment::EnvClaimBroker::BrokerResult
• auto_cuts_ : protocols::environment::AutoCutData
• auto_design : protocols::forge::remodel::RemodelData
• auto_frag_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• auto_loops_ : protocols::protein_interface_design::movers::LoopRemodel
• auto_mm_ : protocols::seeded_abinitio::SegmentHybridizer
• auto_range_ : protocols::matdes::SymDofMover
• auto_tune_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• autofilter_ : protocols::farna::RNA_DeNovoProtocol
• autofilter_score_quantile_ : protocols::farna::RNA_DeNovoProtocol
• autofoldtree_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockProtocol
• autoinitialize_ : protocols::anchored_design::AnchoredDesignMover
• automatic_ : protocols::forge::remodel::RemodelMover::instruction_flags
• automatic_connection_ : protocols::protein_interface_design::movers::TryRotamers
• automatic_distance_cutoff_ : protocols::protein_interface_design::movers::AddChainBreak
• automatic_repacking_definition_ : protocols::simple_moves::DesignRepackMover
• autoset_wt_ : protocols::cryst::SetCrystWeightMover
• autotemp_ : protocols::moves::MonteCarlo
• available_moves_ : protocols::simple_moves::oop::OopRandomPuckMover
• available_seg_list_ : protocols::simple_moves::BBGaussianMover
• average_change_in_rama_score_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• average_change_in_torsion_angle_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• avg : protocols::make_rot_lib::running_average_pair
• avoid_building_any_rotamers_dueto_native_ : protocols::match::upstream::ProteinUpstreamBuilder
• ax_ : 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
• axis_ : protocols::matdes::GetRBDOFValues , protocols::membrane::FlipMover , protocols::rigid::RollMover , protocols::rigid::WholeBodyRotationMover , protocols::simple_moves::UniformRotationMover
• axs : protocols::kinmatch::KRSQuery
• azmiuth_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• azmiuth_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• azmiuth_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern